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HEADER OXYGEN TRANSPORT 16-MAY-94 1FLP TITLE STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM TITLE 2 LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 TITLE 3 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN I (AQUO MET); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUCINA PECTINATA KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.RIZZI,J.B.WITTENBERG,P.ASCENZI,M.FASANO,A.CODA,M.BOLOGNESI REVDAT 1 31-JUL-94 1FLP 0 JRNL AUTH M.RIZZI,J.B.WITTENBERG,A.CODA,M.FASANO,P.ASCENZI, JRNL AUTH 2 M.BOLOGNESI JRNL TITL STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM JRNL TITL 2 THE CLAM LUCINA PECTINATA. CRYSTALLOGRAPHIC JRNL TITL 3 ANALYSIS AT 1.5 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 244 86 1994 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.CASALE,C.LIONETTI,A.CODA,A.MERLI,P.ASCENZI, REMARK 1 AUTH 2 J.B.WITTENBERG,M.BOLOGNESI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DATA FOR THE REMARK 1 TITL 2 FERRIC FORM OF LUCINA PECTINATA HEMOGLOBIN I REMARK 1 REF J.MOL.BIOL. V. 222 447 1991 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.W.KRAUS,J.B.WITTENBERG REMARK 1 TITL HEMOGLOBINS OF THE LUCINA PECTINATA(SLASH)BACTERIA REMARK 1 TITL 2 SYMBIOSIS. I. MOLECULAR PROPERTIES, KINETICS AND REMARK 1 TITL 3 EQUILIBRIA OF REACTIONS WITH LIGANDS REMARK 1 REF J.BIOL.CHEM. V. 265 16043 1990 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARP/WARP, TNT, X-PLOR REMARK 3 AUTHORS : LAMZIN,PERRAKIS,MORRIS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17354 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :NULL REMARK 3 R VALUE (WORKING + TEST SET) :0.170 REMARK 3 R VALUE (WORKING SET) :NULL 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FLP 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 3.101 (2007-05-29) 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: ARP/WARP, X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 19.19500 REMARK 290 SMTRY3 2 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: 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 MET A 142 CA - CB - CG ANGL. DEV. =-26.1 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 203 DISTANCE = 15.38 ANGSTROMS REMARK 525 HOH 204 DISTANCE = 17.23 ANGSTROMS REMARK 525 HOH 212 DISTANCE = 16.24 ANGSTROMS REMARK 525 HOH 214 DISTANCE = 14.61 ANGSTROMS REMARK 525 HOH 220 DISTANCE = 11.14 ANGSTROMS REMARK 525 HOH 222 DISTANCE = 20.48 ANGSTROMS REMARK 525 HOH 228 DISTANCE = 13.72 ANGSTROMS REMARK 525 HOH 231 DISTANCE = 15.48 ANGSTROMS REMARK 525 HOH 232 DISTANCE = 14.40 ANGSTROMS REMARK 525 HOH 233 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH 236 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH 240 DISTANCE = 14.64 ANGSTROMS REMARK 525 HOH 248 DISTANCE = 10.85 ANGSTROMS REMARK 525 HOH 250 DISTANCE = 15.83 ANGSTROMS REMARK 525 HOH 254 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH 257 DISTANCE = 16.71 ANGSTROMS REMARK 525 HOH 267 DISTANCE = 13.42 ANGSTROMS REMARK 525 HOH 275 DISTANCE = 16.25 ANGSTROMS REMARK 525 HOH 276 DISTANCE = 18.40 ANGSTROMS REMARK 525 HOH 287 DISTANCE = 25.85 ANGSTROMS REMARK 525 HOH 293 DISTANCE = 21.30 ANGSTROMS REMARK 525 HOH 294 DISTANCE = 20.27 ANGSTROMS REMARK 525 HOH 299 DISTANCE = 14.48 ANGSTROMS REMARK 525 HOH 300 DISTANCE = 12.94 ANGSTROMS REMARK 525 HOH 301 DISTANCE = 14.81 ANGSTROMS REMARK 525 HOH 307 DISTANCE = 14.75 ANGSTROMS REMARK 525 HOH 308 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH 311 DISTANCE = 11.45 ANGSTROMS REMARK 525 HOH 315 DISTANCE = 22.37 ANGSTROMS REMARK 525 HOH 319 DISTANCE = 11.87 ANGSTROMS REMARK 525 HOH 320 DISTANCE = 17.75 ANGSTROMS REMARK 525 HOH 326 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH 327 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH 328 DISTANCE = 20.47 ANGSTROMS REMARK 525 HOH 332 DISTANCE = 7.96 ANGSTROMS REMARK 525 HOH 336 DISTANCE = 10.05 ANGSTROMS REMARK 525 HOH 345 DISTANCE = 9.06 ANGSTROMS REMARK 525 HOH 346 DISTANCE = 10.98 ANGSTROMS REMARK 525 HOH 347 DISTANCE = 14.95 ANGSTROMS REMARK 525 HOH 349 DISTANCE = 11.12 ANGSTROMS REMARK 525 HOH 350 DISTANCE = 38.45 ANGSTROMS REMARK 525 HOH 352 DISTANCE = 27.92 ANGSTROMS REMARK 525 HOH 354 DISTANCE = 41.10 ANGSTROMS REMARK 525 HOH 360 DISTANCE = 42.52 ANGSTROMS REMARK 525 HOH 362 DISTANCE = 30.07 ANGSTROMS REMARK 525 HOH 364 DISTANCE = 27.17 ANGSTROMS REMARK 525 HOH 365 DISTANCE = 26.16 ANGSTROMS REMARK 525 HOH 378 DISTANCE = 38.65 ANGSTROMS REMARK 525 HOH 380 DISTANCE = 34.05 ANGSTROMS REMARK 525 HOH 382 DISTANCE = 32.57 ANGSTROMS REMARK 525 HOH 383 DISTANCE = 42.97 ANGSTROMS REMARK 525 HOH 384 DISTANCE = 40.98 ANGSTROMS DBREF 1FLP A 1 142 UNP P41260 GLB1_LUCPE 1 142 SEQRES 1 A 142 SER LEU GLU ALA ALA GLN LYS SER ASN VAL THR SER SER SEQRES 2 A 142 TRP ALA LYS ALA SER ALA ALA TRP GLY THR ALA GLY PRO SEQRES 3 A 142 GLU PHE PHE MET ALA LEU PHE ASP ALA HIS ASP ASP VAL SEQRES 4 A 142 PHE ALA LYS PHE SER GLY LEU PHE SER GLY ALA ALA LYS SEQRES 5 A 142 GLY THR VAL LYS ASN THR PRO GLU MET ALA ALA GLN ALA SEQRES 6 A 142 GLN SER PHE LYS GLY LEU VAL SER ASN TRP VAL ASP ASN SEQRES 7 A 142 LEU ASP ASN ALA GLY ALA LEU GLU GLY GLN CYS LYS THR SEQRES 8 A 142 PHE ALA ALA ASN HIS LYS ALA ARG GLY ILE SER ALA GLY SEQRES 9 A 142 GLN LEU GLU ALA ALA PHE LYS VAL LEU SER GLY PHE MET SEQRES 10 A 142 LYS SER TYR GLY GLY ASP GLU GLY ALA TRP THR ALA VAL SEQRES 11 A 142 ALA GLY ALA LEU MET GLY GLU ILE GLU PRO ASP MET FTNOTE 1 THE C-TERMINAL STRETCH 136 - 142 HAS NOT BEEN YET FTNOTE 1 CONFIRMED BY CHEMICAL ANALYSIS. HET HEM 143 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *131(H2 O) HELIX 1 A ALA A 4 ALA A 19 1 16 HELIX 2 B TRP A 21 ALA A 35 1 15 HELIX 3 C ASP A 37 ALA A 41 1 5 HELIX 4 E PRO A 59 VAL A 76 1 18 HELIX 5 F ALA A 82 LYS A 97 1 16 HELIX 6 G ALA A 103 PHE A 116 1 14 HELIX 7 H GLU A 124 ILE A 138 1 15 CRYST1 37.970 38.390 42.650 90.00 97.40 90.00 P 1 21 1 2 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 0.026337 0.000000 0.003421 0.00000 SCALE2 0.000000 0.026048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023644 0.00000