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HEADER OXYGEN TRANSPORT 16-AUG-85 2LHB TITLE REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM TITLE 2 PETROMYZON MARINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN V (CYANO MET); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PETROMYZON MARINUS KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.B.HONZATKO,W.A.HENDRICKSON,W.E.LOVE REVDAT 2 15-APR-91 2LHB 1 HET SITE REVDAT 1 21-JAN-86 2LHB 0 JRNL AUTH R.B.HONZATKO,W.A.HENDRICKSON,W.E.LOVE JRNL TITL REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY JRNL TITL 2 HEMOGLOBIN FROM PETROMYZON MARINUS. JRNL REF J.MOL.BIOL. V. 184 147 1985 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.A.HENDRICKSON,W.E.LOVE,J.KARLE REMARK 1 TITL CRYSTAL STRUCTURE ANALYSIS OF SEA LAMPREY REMARK 1 TITL 2 HEMOGLOBIN AT 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 74 331 1973 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.A.HENDRICKSON,W.E.LOVE REMARK 1 TITL STRUCTURE OF LAMPREY HAEMOGLOBIN REMARK 1 REF NATURE NEW BIOL. V. 232 197 1971 REMARK 1 REFN ASTM NNBYA7 UK ISSN 0369-4887 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LHB COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-23) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.28500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.28500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.31000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 175 O HOH 358 1.65 REMARK 500 O HOH 272 O HOH 316 1.86 REMARK 500 C CYN 150 FE HEM 150 1.90 REMARK 500 O HOH 222 O HOH 292 1.98 REMARK 500 O HOH 211 O HOH 284 2.00 REMARK 500 O HOH 321 O HOH 340 2.04 REMARK 500 CE LYS A 54 O HOH 254 2.05 REMARK 500 OE1 GLU A 63 O HOH 214 2.05 REMARK 500 OD1 ASP A 90 O HOH 264 2.06 REMARK 500 O HOH 220 O HOH 274 2.07 REMARK 500 O HOH 295 O HOH 331 2.07 REMARK 500 O HOH 240 O HOH 318 2.08 REMARK 500 OG1 THR A 126 O HOH 371 2.09 REMARK 500 O HOH 300 O HOH 318 2.09 REMARK 500 NE2 HIS A 105 FE HEM 150 2.10 REMARK 500 OE1 GLU A 75 O HOH 378 2.14 REMARK 500 O HOH 323 O HOH 379 2.16 REMARK 500 NZ LYS A 136 O HOH 375 2.18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH 256 O HOH 322 2565 1.77 REMARK 500 O HOH 164 O HOH 306 2564 1.78 REMARK 500 O HOH 263 O HOH 343 1455 1.84 REMARK 500 O HOH 229 O HOH 241 4455 1.87 REMARK 500 O HOH 276 O HOH 341 4454 2.01 REMARK 500 O HOH 354 O HOH 374 4554 2.01 REMARK 500 O HOH 256 O HOH 331 2565 2.02 REMARK 500 O HOH 223 O HOH 269 4554 2.06 REMARK 500 O HOH 263 O HOH 374 4454 2.06 REMARK 500 O HOH 298 O HOH 343 1455 2.06 REMARK 500 O HOH 287 O HOH 293 2565 2.12 REMARK 500 O HOH 169 O HOH 239 1554 2.14 REMARK 500 O HOH 259 O HOH 315 1455 2.15 REMARK 500 O HOH 156 O HOH 166 2565 2.16 REMARK 500 NH2 ARG A 99 O HOH 193 1556 2.17 REMARK 500 O HOH 185 O HOH 331 2565 2.17 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 99 CG - CD - NE ANGL. DEV. =-31.6 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 193 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH 324 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH 364 DISTANCE = 5.95 ANGSTROMS DBREF 2LHB A 1 149 UNP P02208 GLB5_PETMA 1 149 SEQADV 2LHB GLU A 63 UNP P02208 GLN 63 CONFLICT SEQADV 2LHB ASP A 82 UNP P02208 ASN 82 CONFLICT SEQADV 2LHB ASN A 100 UNP P02208 ASP 100 CONFLICT SEQADV 2LHB GLU A 114 UNP P02208 GLN 114 CONFLICT SEQRES 1 A 149 PRO ILE VAL ASP THR GLY SER VAL ALA PRO LEU SER ALA SEQRES 2 A 149 ALA GLU LYS THR LYS ILE ARG SER ALA TRP ALA PRO VAL SEQRES 3 A 149 TYR SER THR TYR GLU THR SER GLY VAL ASP ILE LEU VAL SEQRES 4 A 149 LYS PHE PHE THR SER THR PRO ALA ALA GLN GLU PHE PHE SEQRES 5 A 149 PRO LYS PHE LYS GLY LEU THR THR ALA ASP GLU LEU LYS SEQRES 6 A 149 LYS SER ALA ASP VAL ARG TRP HIS ALA GLU ARG ILE ILE SEQRES 7 A 149 ASN ALA VAL ASP ASP ALA VAL ALA SER MET ASP ASP THR SEQRES 8 A 149 GLU LYS MET SER MET LYS LEU ARG ASN LEU SER GLY LYS SEQRES 9 A 149 HIS ALA LYS SER PHE GLN VAL ASP PRO GLU TYR PHE LYS SEQRES 10 A 149 VAL LEU ALA ALA VAL ILE ALA ASP THR VAL ALA ALA GLY SEQRES 11 A 149 ASP ALA GLY PHE GLU LYS LEU MET SER MET ILE CYS ILE SEQRES 12 A 149 LEU LEU ARG SER ALA TYR FTNOTE 1 SEE REMARK 5. FTNOTE 2 SEE REMARK 7. HET CYN 150 2 HET HEM 150 43 HETNAM CYN CYANIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 CYN C N 1- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *215(H2 O) HELIX 1 A ALA A 13 SER A 28 1 16 HELIX 2 B TYR A 30 SER A 44 1 15 HELIX 3 C PRO A 46 PHE A 51 5 6 HELIX 4 D ALA A 61 LYS A 66 1 6 HELIX 5 E ALA A 68 ALA A 86 1 19 HELIX 6 F THR A 91 PHE A 109 1 19 HELIX 7 G PRO A 113 VAL A 127 1 15 HELIX 8 H ALA A 132 ALA A 148 1 17 TURN 1 GH ALA A 128 GLY A 130 TYPE II SITE 1 HEM 16 PHE A 52 HIS A 73 ARG A 76 ILE A 77 SITE 2 HEM 16 LEU A 101 SER A 102 LYS A 104 HIS A 105 SITE 3 HEM 16 ALA A 106 PHE A 109 VAL A 111 TYR A 115 SITE 4 HEM 16 PHE A 116 LEU A 119 TYR A 149 HEM 150 CRYST1 44.570 96.620 31.340 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031908 0.00000