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HEADER OXYGEN TRANSPORT 03-DEC-91 1ITH TITLE STRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC TITLE 2 HEMOGLOBIN FROM URECHIS CAUPO AT 2.5 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (CYANO MET); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: URECHIS CAUPO; SOURCE 3 GENE: CDNA KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.HACKERT,P.KOLATKAR,S.R.ERNST,C.M.OGATA,W.A.HENDRICKSON, AUTHOR 2 E.A.MERRITT,R.P.PHIZACKERLEY REVDAT 2 01-APR-03 1ITH 1 JRNL REVDAT 1 31-OCT-93 1ITH 0 JRNL AUTH P.R.KOLATKAR,S.R.ERNST,M.L.HACKERT,C.M.OGATA, JRNL AUTH 2 W.A.HENDRICKSON,E.A.MERRITT,R.P.PHIZACKERLEY JRNL TITL STRUCTURE DETERMINATION AND REFINEMENT OF JRNL TITL 2 HOMOTETRAMERIC HEMOGLOBIN FROM URECHIS CAUPO AT JRNL TITL 3 2.5 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR., SECT.B V. 48 191 1992 JRNL REFN ASTM ASBSDK DK ISSN 0108-7681 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.KOLATKAR,W.E.MEADOR,R.L.STANFIELD,M.L.HACKERT REMARK 1 TITL NOVEL SUBUNIT STRUCTURE OBSERVED FOR REMARK 1 TITL 2 NONCOOPERATIVE HEMOGLOBIN FROM URECHIS CAUPO REMARK 1 REF J.BIOL.CHEM. V. 263 3462 1988 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 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) : 0.147 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 : 2126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 150 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.33 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 1ITH 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: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 -X,Y,1/2-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 1/2+X,1/2+Y,Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-X,1/2+Y,1/2-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.40000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.45000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.40000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.45000 REMARK 290 SMTRY3 8 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 2 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, B 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 54.90000 REMARK 350 BIOMT3 2 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 NE2 HIS A 94 FE HEM A 1 2.16 REMARK 500 NE2 HIS B 94 FE HEM B 1 2.16 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 606 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH 631 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH 633 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH 638 DISTANCE = 5.43 ANGSTROMS DBREF 1ITH A 1 141 UNP P06148 HBF1_URECA 1 141 DBREF 1ITH B 1 141 UNP P06148 HBF1_URECA 1 141 SEQADV 1ITH ALA A 4 UNP P06148 THR 4 CONFLICT SEQADV 1ITH ALA B 4 UNP P06148 THR 4 CONFLICT SEQRES 1 A 141 GLY LEU THR ALA ALA GLN ILE LYS ALA ILE GLN ASP HIS SEQRES 2 A 141 TRP PHE LEU ASN ILE LYS GLY CYS LEU GLN ALA ALA ALA SEQRES 3 A 141 ASP SER ILE PHE PHE LYS TYR LEU THR ALA TYR PRO GLY SEQRES 4 A 141 ASP LEU ALA PHE PHE HIS LYS PHE SER SER VAL PRO LEU SEQRES 5 A 141 TYR GLY LEU ARG SER ASN PRO ALA TYR LYS ALA GLN THR SEQRES 6 A 141 LEU THR VAL ILE ASN TYR LEU ASP LYS VAL VAL ASP ALA SEQRES 7 A 141 LEU GLY GLY ASN ALA GLY ALA LEU MET LYS ALA LYS VAL SEQRES 8 A 141 PRO SER HIS ASP ALA MET GLY ILE THR PRO LYS HIS PHE SEQRES 9 A 141 GLY GLN LEU LEU LYS LEU VAL GLY GLY VAL PHE GLN GLU SEQRES 10 A 141 GLU PHE SER ALA ASP PRO THR THR VAL ALA ALA TRP GLY SEQRES 11 A 141 ASP ALA ALA GLY VAL LEU VAL ALA ALA MET LYS SEQRES 1 B 141 GLY LEU THR ALA ALA GLN ILE LYS ALA ILE GLN ASP HIS SEQRES 2 B 141 TRP PHE LEU ASN ILE LYS GLY CYS LEU GLN ALA ALA ALA SEQRES 3 B 141 ASP SER ILE PHE PHE LYS TYR LEU THR ALA TYR PRO GLY SEQRES 4 B 141 ASP LEU ALA PHE PHE HIS LYS PHE SER SER VAL PRO LEU SEQRES 5 B 141 TYR GLY LEU ARG SER ASN PRO ALA TYR LYS ALA GLN THR SEQRES 6 B 141 LEU THR VAL ILE ASN TYR LEU ASP LYS VAL VAL ASP ALA SEQRES 7 B 141 LEU GLY GLY ASN ALA GLY ALA LEU MET LYS ALA LYS VAL SEQRES 8 B 141 PRO SER HIS ASP ALA MET GLY ILE THR PRO LYS HIS PHE SEQRES 9 B 141 GLY GLN LEU LEU LYS LEU VAL GLY GLY VAL PHE GLN GLU SEQRES 10 B 141 GLU PHE SER ALA ASP PRO THR THR VAL ALA ALA TRP GLY SEQRES 11 B 141 ASP ALA ALA GLY VAL LEU VAL ALA ALA MET LYS HET CYN A 101 2 HET CYN B 101 2 HET HEM A 1 43 HET HEM B 1 43 HETNAM CYN CYANIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 CYN 2(C N 1-) FORMUL 5 HEM 2(C34 H32 FE N4 O4) FORMUL 7 HOH *150(H2 O) HELIX 1 AA THR A 3 ASN A 17 1 15 HELIX 2 BA LEU A 22 TYR A 37 1 16 HELIX 3 CA PRO A 38 PHE A 43 5 6 HELIX 4 DA PRO A 51 LEU A 55 5 5 HELIX 5 EA ASN A 58 ALA A 78 1 21 HELIX 6 F1A GLY A 81 ALA A 89 1 9 HELIX 7 F2A LYS A 88 VAL A 91 5 4 HELIX 8 F3A VAL A 91 ALA A 96 1 6 HELIX 9 GA THR A 100 GLU A 118 1GLY 112/GLY 113 FORM A KINK 19 HELIX 10 HA ASP A 122 ALA A 139 1 18 HELIX 11 AB THR B 3 ASN B 17 1 15 HELIX 12 BB LEU B 22 TYR B 37 1 16 HELIX 13 CB PRO B 38 PHE B 43 5 6 HELIX 14 DB PRO B 51 LEU B 55 5 5 HELIX 15 EB ASN B 58 ALA B 78 1 21 HELIX 16 F1B GLY B 81 ALA B 89 1 9 HELIX 17 F2B LYS B 88 VAL B 91 5 4 HELIX 18 F3B VAL B 91 ALA B 96 1 6 HELIX 19 GB THR B 100 GLU B 118 1GLY 112/GLY 113 FORM A KINK 19 HELIX 20 HB ASP B 122 ALA B 139 1 18 LINK C CYN A 101 FE HEM A 1 LINK C CYN B 101 FE HEM B 1 CRYST1 104.800 54.900 110.600 90.00 90.00 90.00 C 2 2 21 16 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 0.009542 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009042 0.00000 MTRIX1 1 -1.000000 -0.002700 -0.000700 49.96160 1 MTRIX2 1 0.000400 -0.373700 0.927600 37.66540 1 MTRIX3 1 -0.002700 0.927600 0.373700 -25.28980 1