HEADER OXYGEN TRANSPORT 04-NOV-98 1EBT TITLE HEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA BOUND WITH CYANIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUCINA PECTINATA; SOURCE 3 ORGANISM_TAXID: 29163 KEYWDS OXYGEN TRANSPORT, HEMOGLOBIN, OXYGEN CARRIER, GLOBIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ROSANO,M.BOLOGNESI,P.ASCENZI REVDAT 4 09-AUG-23 1EBT 1 REMARK LINK REVDAT 3 24-FEB-09 1EBT 1 VERSN REVDAT 2 12-APR-05 1EBT 1 JRNL REMARK REVDAT 1 13-JAN-00 1EBT 0 JRNL AUTH M.BOLOGNESI,C.ROSANO,R.LOSSO,A.BORASSI,M.RIZZI, JRNL AUTH 2 J.B.WITTENBERG,A.BOFFI,P.ASCENZI JRNL TITL CYANIDE BINDING TO LUCINA PECTINATA HEMOGLOBIN I AND TO JRNL TITL 2 SPERM WHALE MYOGLOBIN: AN X-RAY CRYSTALLOGRAPHIC STUDY. JRNL REF BIOPHYS.J. V. 77 1093 1999 JRNL REFN ISSN 0006-3495 JRNL PMID 10423453 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 12085 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) : NULL 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) : 0.1840 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1208 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12085 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1036 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 79 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) : 0.015 ; 1.500 ; 1106 REMARK 3 BOND ANGLES (DEGREES) : 2.397 ; 2.000 ; 1486 REMARK 3 TORSION ANGLES (DEGREES) : 14.176; 0.000 ; 637 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.016 ; 2.500 ; 28 REMARK 3 GENERAL PLANES (A) : 0.011 ; 9.000 ; 163 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.321 ; 10.000; 1059 REMARK 3 NON-BONDED CONTACTS (A) : 0.062 ; 15.000; 11 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.84 REMARK 3 BSOL : 57.80 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EBT 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_1000172999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-95 REMARK 200 TEMPERATURE (KELVIN) : 300.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.200 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1FLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00 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 19.38000 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 ASP A 37 OD1 OD2 REMARK 480 GLN A 66 CD NE2 REMARK 480 ASN A 74 CG REMARK 480 LYS A 90 CD CE NZ REMARK 480 LYS A 97 CE NZ REMARK 480 LYS A 111 CD CE NZ REMARK 480 LYS A 118 NZ REMARK 480 GLU A 139 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 27 CD GLU A 27 OE2 0.077 REMARK 500 GLU A 86 CD GLU A 86 OE2 0.068 REMARK 500 GLU A 137 CD GLU A 137 OE1 -0.069 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 38 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 77 CB - CG - OD1 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP A 77 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 80 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 80 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -5.0 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 144 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HEM A 144 NA 94.0 REMARK 620 3 HEM A 144 NB 90.7 86.8 REMARK 620 4 HEM A 144 NC 85.5 177.3 90.5 REMARK 620 5 HEM A 144 ND 89.4 95.5 177.7 87.2 REMARK 620 6 CYN A 145 C 170.6 95.2 91.6 85.3 88.0 REMARK 620 7 CYN A 145 N 162.0 70.5 79.7 109.5 100.9 27.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYN A 145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 144 DBREF 1EBT A 1 142 UNP P41260 GLB1_LUCPE 1 142 SEQADV 1EBT SER A 3 UNP P41260 GLU 3 SEE REMARK 999 SEQADV 1EBT ASP A 8 UNP P41260 SER 8 SEE REMARK 999 SEQADV 1EBT ASN A 141 UNP P41260 ASP 141 SEE REMARK 999 SEQRES 1 A 142 SER LEU SER ALA ALA GLN LYS ASP 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 ASN MET HET CYN A 145 2 HET HEM A 144 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 *79(H2 O) HELIX 1 1 ALA A 4 ALA A 19 1 16 HELIX 2 2 TRP A 21 ALA A 35 1 15 HELIX 3 3 ASP A 37 PHE A 43 1 7 HELIX 4 4 LYS A 52 THR A 54 5 3 HELIX 5 5 PRO A 59 ASN A 78 1 20 HELIX 6 6 ALA A 82 ARG A 99 1 18 HELIX 7 7 ALA A 103 TYR A 120 1 18 HELIX 8 8 GLU A 124 ILE A 138 1 15 LINK NE2 HIS A 96 FE HEM A 144 1555 1555 2.15 LINK FE HEM A 144 C CYN A 145 1555 1555 2.54 LINK FE HEM A 144 N CYN A 145 1555 1555 2.66 SITE 1 AC1 3 PHE A 43 GLN A 64 HEM A 144 SITE 1 AC2 12 LYS A 42 PHE A 43 GLN A 64 SER A 67 SITE 2 AC2 12 PHE A 68 PHE A 92 ASN A 95 HIS A 96 SITE 3 AC2 12 ARG A 99 ILE A 101 CYN A 145 HOH A 504 CRYST1 50.670 38.760 42.530 90.00 106.93 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 0.019736 0.000000 0.006007 0.00000 SCALE2 0.000000 0.025800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024578 0.00000