HEADER OXYGEN TRANSPORT 16-MAY-94 1FLP TITLE STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA TITLE 2 PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 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; SOURCE 3 ORGANISM_TAXID: 29163 KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.RIZZI,J.B.WITTENBERG,P.ASCENZI,M.FASANO,A.CODA,M.BOLOGNESI REVDAT 3 07-FEB-24 1FLP 1 REMARK LINK REVDAT 2 24-FEB-09 1FLP 1 VERSN REVDAT 1 31-JUL-94 1FLP 0 JRNL AUTH M.RIZZI,J.B.WITTENBERG,A.CODA,M.FASANO,P.ASCENZI,M.BOLOGNESI JRNL TITL STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM JRNL TITL 2 LUCINA PECTINATA. CRYSTALLOGRAPHIC ANALYSIS AT 1.5 A JRNL TITL 3 RESOLUTION. JRNL REF J.MOL.BIOL. V. 244 86 1994 JRNL REFN ISSN 0022-2836 JRNL PMID 7966324 JRNL DOI 10.1006/JMBI.1994.1706 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.CASALE,C.LIONETTI,A.CODA,A.MERLI,P.ASCENZI,J.B.WITTENBERG, REMARK 1 AUTH 2 M.BOLOGNESI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DATA FOR THE FERRIC FORM OF REMARK 1 TITL 2 LUCINA PECTINATA HEMOGLOBIN I REMARK 1 REF J.MOL.BIOL. V. 222 447 1991 REMARK 1 REFN 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 EQUILIBRIA REMARK 1 TITL 3 OF REACTIONS WITH LIGANDS REMARK 1 REF J.BIOL.CHEM. V. 265 16043 1990 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173333. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 (%): 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,Y+1/2,-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 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 16 CE NZ REMARK 480 GLU A 86 OE1 OE2 REMARK 480 LYS A 90 CD CE NZ REMARK 480 LYS A 111 CD CE NZ 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 3 OE1 - CD - OE2 ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 MET A 142 CA - CB - CG ANGL. DEV. = -25.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 143 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HEM A 143 NA 89.3 REMARK 620 3 HEM A 143 NB 92.3 88.9 REMARK 620 4 HEM A 143 NC 91.2 177.5 88.6 REMARK 620 5 HEM A 143 ND 93.1 91.6 174.6 90.8 REMARK 620 6 HOH A 202 O 177.7 90.9 85.4 88.5 89.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 143 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DETERMINED BY REMARK 999 D. WALTZ AND S. VINOGRADOV. 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 HET HEM A 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 LINK NE2 HIS A 96 FE HEM A 143 1555 1555 2.31 LINK FE HEM A 143 O HOH A 202 1555 1555 2.28 SITE 1 AC1 15 LYS A 42 PHE A 43 SER A 67 PHE A 68 SITE 2 AC1 15 PHE A 92 ASN A 95 HIS A 96 ARG A 99 SITE 3 AC1 15 ILE A 101 GLN A 105 PHE A 110 HOH A 202 SITE 4 AC1 15 HOH A 210 HOH A 221 HOH A 373 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