PDB Short entry for 1DWL HEADER ELECTRON TRANSFER 08-DEC-99 1DWL TITLE THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR TITLE 2 AND DOCKING SIMULATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CONTAINS A FE4S4 CLUSTER COVALENTLY LINKED COMPND 6 BY FOUR CYSTEINS; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYTOCHROME C553; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: LOW POTENTIAL CYTOCHROME C; COMPND 11 OTHER_DETAILS: CONTAINS A HEME GROUP COVALENTLY LINKED BY COMPND 12 2 CYSTEINES AND THE IRON ATOM IS COORDINATED BY A COMPND 13 HISTIDINE AND A METHIONINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOMICROBIUM NORVEGICUM; SOURCE 3 ORGANISM_TAXID: 52561; SOURCE 4 CELLULAR_LOCATION: PERIPLASM; SOURCE 5 PLASMID: PETFDI; SOURCE 6 GENE: FDXI; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 12 ORGANISM_TAXID: 882; SOURCE 13 STRAIN: HILDENBOROUGH; SOURCE 14 CELLULAR_LOCATION: CYTOPLASM KEYWDS ELECTRON TRANSFER, FERREDOXIN-CYTOCHROME COMPLEX, MODEL, KEYWDS 2 HETERONUCLEAR NMR, DOCKING EXPDTA SOLUTION NMR; THEORETICAL MODEL NUMMDL 3 AUTHOR X.MORELLI,F.GUERLESQUIN,M.CZJZEK,P.N.PALMA REVDAT 5 24-FEB-09 1DWL 1 VERSN REVDAT 4 01-SEP-00 1DWL 1 DBREF REVDAT 3 08-JUL-00 1DWL 1 REMARK REVDAT 2 10-APR-00 1DWL 1 JRNL REVDAT 1 10-DEC-99 1DWL 0 JRNL AUTH X.MORELLI,A.DOLLA,M.CZJZEK,P.N.PALMA,F.BLASCO, JRNL AUTH 2 L.KRIPPAHL,J.J.G.MOURA,F.GUERLESQUIN JRNL TITL HETERONUCLEAR NMR AND SOFT DOCKING: AN JRNL TITL 2 EXPERIMENTAL APPROACH FOR A STRUCTURAL MODEL OF JRNL TITL 3 THE CYTOCHROME C553-FERREDOXIN COMPLEX JRNL REF BIOCHEMISTRY V. 39 2530 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10704202 JRNL DOI 10.1021/BI992306S REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.N.PALMA,L.KRIPPAHL,J.E.WAMPLER,J.J.G.MOURA REMARK 1 TITL BIGGER: A NEW (SOFT) DOCKING ALGORITHM FOR REMARK 1 TITL 2 PREDICTING PROTEIN INTERACTIONS REMARK 1 REF PROTEINS: STRUCT.,FUNCT., V. 39 372 2000 REMARK 1 REF 2 GENET. REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 10813819 REMARK 1 DOI 10.1002/(SICI)1097-0134(20000601)39:4<372::AI REMARK 1 DOI 2 D-PROT100>3.3.CO;2-H REMARK 1 REFERENCE 2 REMARK 1 AUTH X.MORELLI,F.GUERLESQUIN REMARK 1 TITL MAPPING THE CYTOCHROME C553 INTERACTING SITE USING REMARK 1 TITL 2 1H AND 15N NMR REMARK 1 REF FEBS LETT. V. 460 77 1999 REMARK 1 REFN ISSN 0014-5793 REMARK 1 PMID 10571064 REMARK 1 DOI 10.1016/S0014-5793(99)01299-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS CALCULATION USING REMARK 3 AMBER FORCE FIELD THESE ARE 3 MODEL STRUCTURES FOR THE COMPLEX REMARK 3 OF CYTOCHROME C553 WITH FERREDOXIN I REMARK 4 REMARK 4 1DWL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-99. REMARK 100 THE PDBE ID CODE IS EBI-4450. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 5.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 10% D2O/90% WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MAPPING OF THE CHEMICAL REMARK 210 SHIFT VARIATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 3 REMARK 210 CONFORMERS, SELECTION CRITERIA : COMBINATION OF NMR SHIFT REMARK 210 VARIATION AND A SOFT REMARK 210 DOCKING ALGORITHM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 REMARK 210 REMARK 210 REMARK: HETERONUCLEAR EXPERIMENTS ON 15N-LABELED FERREDOXIN REMARK 210 AND CYTOCHROME, CHEMICAL SHIFT VARIATION ANALYSIS REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 MODELLING PROGRAM : BIGGER REMARK 220 PROGRAM AUTHORS : P.N. PALMA REMARK 220 REMARK 220 REMARK: MODELLING EXPERIMENT: THE COMPLEX STRUCTURE WAS OBTAINED REMARK 220 BY SOFT DOCKING ALGORITHM IMPLEMENTED WITH AN NMR FILTER. REMARK 220 THE STARTING MODELS OF THE CYTOCHROME AND THE FERREDOXIN REMARK 220 WERE BASED ON THE PDB ENTRIES 1DVH AND 1FXD REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 DISTANCE REMARK 500 HD1 HIS B 14 - O LYS B 20 1.59 REMARK 500 CG MET B 23 - CG ARG B 53 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 1 GLY A 11 C CYS A 12 N -0.198 REMARK 500 1 SER A 14 C CYS A 15 N -0.341 REMARK 500 1 GLU B 67 N GLU B 67 CA 0.130 REMARK 500 1 TYR B 75 C MET B 76 N 0.194 REMARK 500 2 ALA B 21 C ALA B 22 N 0.197 REMARK 500 2 GLY B 24 C SER B 25 N 0.211 REMARK 500 2 SER B 65 C SER B 65 O 0.127 REMARK 500 2 SER B 65 C ASP B 66 N 0.194 REMARK 500 2 LYS B 78 C LEU B 79 N 0.257 REMARK 500 3 SER A 14 N SER A 14 CA 0.120 REMARK 500 3 GLY B 24 C SER B 25 N 0.244 REMARK 500 3 TYR B 64 C SER B 65 N -0.298 REMARK 500 3 ASP B 66 C GLU B 67 N 0.164 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 1 GLY A 11 CA - C - N ANGL. DEV. = 25.3 DEGREES REMARK 500 1 GLY A 11 O - C - N ANGL. DEV. = -26.7 DEGREES REMARK 500 1 CYS A 12 C - N - CA ANGL. DEV. = 29.9 DEGREES REMARK 500 1 SER A 14 CA - C - N ANGL. DEV. = 25.7 DEGREES REMARK 500 1 SER A 14 O - C - N ANGL. DEV. = -28.3 DEGREES REMARK 500 1 CYS A 15 C - N - CA ANGL. DEV. = 28.1 DEGREES REMARK 500 1 GLU A 29 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 1 GLU A 59 N - CA - C ANGL. DEV. = -19.2 DEGREES REMARK 500 1 CYS B 13 CA - CB - SG ANGL. DEV. = -6.8 DEGREES REMARK 500 1 GLY B 24 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 1 MET B 23 CA - C - N ANGL. DEV. = -15.7 DEGREES REMARK 500 1 MET B 23 O - C - N ANGL. DEV. = 19.4 DEGREES REMARK 500 1 GLY B 24 C - N - CA ANGL. DEV. = 14.4 DEGREES REMARK 500 1 ASP B 66 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 1 TYR B 75 CA - C - N ANGL. DEV. = -14.5 DEGREES REMARK 500 1 TYR B 75 O - C - N ANGL. DEV. = 20.6 DEGREES REMARK 500 1 LEU B 79 N - CA - C ANGL. DEV. = -17.2 DEGREES REMARK 500 2 CYS A 9 CA - CB - SG ANGL. DEV. = -11.1 DEGREES REMARK 500 2 CYS A 9 CA - CB - SG ANGL. DEV. = -10.9 DEGREES REMARK 500 2 GLU A 29 O - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 2 CYS A 51 CA - CB - SG ANGL. DEV. = -11.8 DEGREES REMARK 500 2 CYS A 51 CA - CB - SG ANGL. DEV. = -11.6 DEGREES REMARK 500 2 GLU A 59 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 2 GLY B 15 C - N - CA ANGL. DEV. = -13.4 DEGREES REMARK 500 2 ALA B 21 CA - C - N ANGL. DEV. = -16.0 DEGREES REMARK 500 2 ALA B 21 O - C - N ANGL. DEV. = 16.1 DEGREES REMARK 500 2 ALA B 22 C - N - CA ANGL. DEV. = -28.8 DEGREES REMARK 500 2 ALA B 22 O - C - N ANGL. DEV. = 11.4 DEGREES REMARK 500 2 GLY B 24 CA - C - N ANGL. DEV. = -17.8 DEGREES REMARK 500 2 GLY B 24 O - C - N ANGL. DEV. = -20.6 DEGREES REMARK 500 2 SER B 25 C - N - CA ANGL. DEV. = 28.7 DEGREES REMARK 500 2 SER B 65 CA - C - N ANGL. DEV. = -21.3 DEGREES REMARK 500 2 SER B 65 O - C - N ANGL. DEV. = 26.5 DEGREES REMARK 500 2 ASP B 66 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 2 TYR B 75 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 LEU B 79 N - CA - C ANGL. DEV. = -17.2 DEGREES REMARK 500 2 LYS B 78 CA - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 2 LYS B 78 O - C - N ANGL. DEV. = 12.9 DEGREES REMARK 500 3 CYS A 19 CA - CB - SG ANGL. DEV. = -8.1 DEGREES REMARK 500 3 SER A 39 N - CA - CB ANGL. DEV. = -9.2 DEGREES REMARK 500 3 CYS A 51 CA - CB - SG ANGL. DEV. = -7.8 DEGREES REMARK 500 3 GLU A 59 N - CA - C ANGL. DEV. = -18.6 DEGREES REMARK 500 3 ALA B 4 O - C - N ANGL. DEV. = -13.2 DEGREES REMARK 500 3 CYS B 13 CA - CB - SG ANGL. DEV. = -8.4 DEGREES REMARK 500 3 GLU B 67 O - C - N ANGL. DEV. = 14.1 DEGREES REMARK 500 3 LEU B 79 N - CA - C ANGL. DEV. = -18.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLU A 13 -4.27 70.69 REMARK 500 1 SER A 14 -78.99 -51.78 REMARK 500 1 GLU A 29 5.14 47.03 REMARK 500 1 GLU A 30 -15.64 -147.09 REMARK 500 1 SER A 39 98.57 -69.62 REMARK 500 1 THR A 40 66.63 -65.55 REMARK 500 1 ALA A 50 20.78 -151.75 REMARK 500 1 LYS B 54 3.39 31.70 REMARK 500 1 TYR B 64 67.33 -106.51 REMARK 500 1 SER B 65 77.44 -57.16 REMARK 500 1 ASP B 74 86.75 -69.66 REMARK 500 1 TYR B 75 -53.29 -161.83 REMARK 500 1 MET B 76 79.90 -67.31 REMARK 500 1 SER B 77 40.63 -146.39 REMARK 500 2 GLU A 8 36.59 -163.99 REMARK 500 2 CYS A 9 66.77 -101.88 REMARK 500 2 GLU A 13 -17.50 36.65 REMARK 500 2 SER A 14 -82.32 -45.49 REMARK 500 2 VAL A 22 -53.09 -136.28 REMARK 500 2 GLU A 29 -3.30 54.39 REMARK 500 2 ASP A 38 -53.36 -129.88 REMARK 500 2 ALA B 16 -2.87 33.59 REMARK 500 2 SER B 19 42.97 -94.87 REMARK 500 2 SER B 25 61.29 37.37 REMARK 500 2 ARG B 53 44.09 -97.29 REMARK 500 2 SER B 65 93.22 -40.87 REMARK 500 2 ASP B 66 7.53 41.43 REMARK 500 2 ALA B 71 -53.74 -138.42 REMARK 500 2 ASP B 74 -54.53 -155.72 REMARK 500 2 LYS B 78 -56.37 -138.01 REMARK 500 3 GLU A 13 -61.64 17.82 REMARK 500 3 SER A 14 -84.29 18.19 REMARK 500 3 VAL A 22 -58.69 -135.94 REMARK 500 3 GLU A 29 15.28 54.14 REMARK 500 3 GLU A 30 -3.93 -167.63 REMARK 500 3 SER A 39 82.31 -65.39 REMARK 500 3 THR A 40 77.19 -66.01 REMARK 500 3 ALA B 4 -92.27 11.63 REMARK 500 3 LEU B 6 44.44 -85.98 REMARK 500 3 LYS B 8 -83.62 12.15 REMARK 500 3 ALA B 22 41.12 -90.05 REMARK 500 3 SER B 25 -165.08 67.02 REMARK 500 3 ALA B 26 -178.81 166.88 REMARK 500 3 PRO B 28 108.56 -58.80 REMARK 500 3 ALA B 34 -27.19 34.59 REMARK 500 3 ARG B 53 54.65 -91.61 REMARK 500 3 TYR B 64 67.41 -113.98 REMARK 500 3 ASP B 66 -22.13 38.73 REMARK 500 3 GLU B 67 71.65 -169.45 REMARK 500 3 GLU B 68 -35.70 -147.85 REMARK 500 3 ALA B 71 51.28 -113.99 REMARK 500 3 TYR B 75 -50.43 -171.99 REMARK 500 3 LYS B 78 -39.36 -161.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 4 ASP A 5 1 -148.20 REMARK 500 ASP A 5 HIS A 6 1 142.91 REMARK 500 GLY A 11 CYS A 12 1 51.64 REMARK 500 CYS A 19 PRO A 20 1 -141.95 REMARK 500 GLU A 54 ALA A 55 1 -149.22 REMARK 500 LYS B 20 ALA B 21 1 142.08 REMARK 500 TYR B 64 SER B 65 1 -146.69 REMARK 500 SER B 65 ASP B 66 1 124.87 REMARK 500 LYS B 78 LEU B 79 1 141.35 REMARK 500 GLY A 11 CYS A 12 2 -78.59 REMARK 500 CYS A 19 PRO A 20 2 -147.36 REMARK 500 CYS A 51 PRO A 52 2 -143.11 REMARK 500 CYS B 10 ILE B 11 2 -149.70 REMARK 500 MET B 76 SER B 77 2 137.59 REMARK 500 GLY A 11 CYS A 12 3 -129.02 REMARK 500 CYS A 51 PRO A 52 3 -147.18 REMARK 500 ALA B 21 ALA B 22 3 -144.85 REMARK 500 GLY B 24 SER B 25 3 -149.34 REMARK 500 GLN B 32 GLY B 33 3 145.34 REMARK 500 TYR B 64 SER B 65 3 -134.78 REMARK 500 LYS B 78 LEU B 79 3 140.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR B 64 0.13 SIDE CHAIN REMARK 500 2 TYR B 49 0.09 SIDE CHAIN REMARK 500 2 TYR B 75 0.30 SIDE CHAIN REMARK 500 3 TYR B 7 0.08 SIDE CHAIN REMARK 500 3 TYR B 44 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 MET B 76 11.62 REMARK 500 2 ASP B 17 -10.17 REMARK 500 2 GLY B 24 -30.30 REMARK 500 3 GLY B 24 20.42 REMARK 500 3 TYR B 64 -10.79 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 SF4 A 60 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 SF4 A 60 FE3 142.7 REMARK 620 3 SF4 A 60 S2 106.0 56.7 REMARK 620 4 SF4 A 60 FE4 141.0 62.0 57.3 REMARK 620 5 SF4 A 60 FE2 148.1 61.1 105.9 60.5 REMARK 620 6 SF4 A 60 S3 109.9 107.2 110.5 57.1 56.5 REMARK 620 7 SF4 A 60 S4 112.6 56.8 109.6 106.4 56.6 108.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 60 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SF4 A 60 FE3 REMARK 620 2 SF4 A 60 S2 55.5 REMARK 620 3 SF4 A 60 FE1 59.2 56.7 REMARK 620 4 SF4 A 60 FE2 60.2 105.4 60.5 REMARK 620 5 SF4 A 60 S3 104.5 109.5 56.7 56.4 REMARK 620 6 SF4 A 60 S1 55.4 106.2 104.0 56.3 109.3 REMARK 620 7 CYS A 12 SG 150.0 109.7 139.1 144.4 105.1 116.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 60 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 SF4 A 60 S2 108.7 REMARK 620 3 SF4 A 60 FE1 143.7 56.8 REMARK 620 4 SF4 A 60 FE4 145.5 56.1 58.9 REMARK 620 5 SF4 A 60 FE2 146.2 105.1 60.0 59.1 REMARK 620 6 SF4 A 60 S4 110.7 109.6 56.7 103.8 56.2 REMARK 620 7 SF4 A 60 S1 112.0 107.4 104.3 56.1 56.1 108.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 60 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SF4 A 60 FE3 REMARK 620 2 CYS A 51 SG 145.6 REMARK 620 3 SF4 A 60 FE1 58.9 144.0 REMARK 620 4 SF4 A 60 FE4 60.7 145.3 59.0 REMARK 620 5 SF4 A 60 S3 105.1 109.2 56.2 56.5 REMARK 620 6 SF4 A 60 S4 55.8 109.8 56.1 104.8 107.5 REMARK 620 7 SF4 A 60 S1 55.7 112.9 103.1 56.6 109.7 107.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 80 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HEC B 80 NC REMARK 620 2 HEC B 80 NB 89.3 REMARK 620 3 HEC B 80 ND 89.7 178.9 REMARK 620 4 MET B 57 SD 89.9 87.6 92.1 REMARK 620 5 HIS B 14 NE2 91.7 92.5 87.8 178.4 REMARK 620 6 HEC B 80 NA 178.4 90.6 90.5 91.6 86.8 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 SF4 A 60 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC B 80 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DVH RELATED DB: PDB REMARK 900 CYTOCHROME C553 (REDUCED) (NMR, 36 STRUCTURES) REMARK 900 RELATED ID: 2DVH RELATED DB: PDB REMARK 900 THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO REMARK 900 VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES REMARK 900 RELATED ID: 1FXD RELATED DB: PDB REMARK 900 FERREDOXIN II OF DESULFOVIBRIO GIGAS (CRYSTAL STRUCTURE) DBREF 1DWL A 1 59 UNP P07485 FER1_DESDN 1 59 DBREF 1DWL B 1 79 UNP P04032 C553_DESVH 25 103 SEQRES 1 A 59 THR ILE VAL ILE ASP HIS GLU GLU CYS ILE GLY CYS GLU SEQRES 2 A 59 SER CYS VAL GLU LEU CYS PRO GLU VAL PHE ALA MET ILE SEQRES 3 A 59 ASP GLY GLU GLU LYS ALA MET VAL THR ALA PRO ASP SER SEQRES 4 A 59 THR ALA GLU CYS ALA GLN ASP ALA ILE ASP ALA CYS PRO SEQRES 5 A 59 VAL GLU ALA ILE SER LYS GLU SEQRES 1 B 79 ALA ASP GLY ALA ALA LEU TYR LYS SER CYS ILE GLY CYS SEQRES 2 B 79 HIS GLY ALA ASP GLY SER LYS ALA ALA MET GLY SER ALA SEQRES 3 B 79 LYS PRO VAL LYS GLY GLN GLY ALA GLU GLU LEU TYR LYS SEQRES 4 B 79 LYS MET LYS GLY TYR ALA ASP GLY SER TYR GLY GLY GLU SEQRES 5 B 79 ARG LYS ALA MET MET THR ASN ALA VAL LYS LYS TYR SER SEQRES 6 B 79 ASP GLU GLU LEU LYS ALA LEU ALA ASP TYR MET SER LYS SEQRES 7 B 79 LEU HET SF4 A 60 8 HET HEC B 80 47 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM HEC HEME C FORMUL 3 SF4 FE4 S4 2+ FORMUL 4 HEC C34 H34 FE N4 O4 HELIX 1 1 GLU A 13 LEU A 18 5 6 HELIX 2 2 ALA A 41 ASP A 46 5 6 HELIX 3 3 ASP A 46 CYS A 51 5 6 HELIX 4 4 ASP B 2 TYR B 7 5 6 HELIX 5 5 CYS B 10 GLY B 15 1 6 HELIX 6 6 GLY B 33 ASP B 46 1 14 HELIX 7 7 LYS B 54 TYR B 64 1 11 HELIX 8 8 GLU B 67 ALA B 73 1 7 SHEET 1 A 2 ILE A 2 ILE A 4 0 SHEET 2 A 2 ILE A 56 LYS A 58 -1 O SER A 57 N VAL A 3 SHEET 1 B 2 PHE A 23 ASP A 27 0 SHEET 2 B 2 ALA A 32 VAL A 34 -1 O MET A 33 N ALA A 24 LINK FE1 SF4 A 60 SG CYS A 9 1555 1555 2.32 LINK FE4 SF4 A 60 SG CYS A 12 1555 1555 2.28 LINK FE3 SF4 A 60 SG CYS A 15 1555 1555 2.34 LINK FE2 SF4 A 60 SG CYS A 51 1555 1555 2.34 LINK SG CYS B 10 CAB HEC B 80 1555 1555 1.83 LINK SG CYS B 13 CAC HEC B 80 1555 1555 1.83 LINK FE HEC B 80 NE2 HIS B 14 1555 1555 2.17 LINK FE HEC B 80 SD MET B 57 1555 1555 2.33 SITE 1 AC1 12 ILE A 4 CYS A 9 GLY A 11 CYS A 12 SITE 2 AC1 12 GLU A 13 SER A 14 CYS A 15 ASP A 27 SITE 3 AC1 12 ALA A 47 ALA A 50 CYS A 51 PRO A 52 SITE 1 AC2 24 CYS A 12 SER A 14 TYR B 7 CYS B 10 SITE 2 AC2 24 CYS B 13 HIS B 14 MET B 23 ALA B 26 SITE 3 AC2 24 LYS B 27 VAL B 29 LEU B 37 LYS B 40 SITE 4 AC2 24 MET B 41 TYR B 44 TYR B 49 GLY B 51 SITE 5 AC2 24 GLU B 52 ARG B 53 LYS B 54 MET B 56 SITE 6 AC2 24 MET B 57 TYR B 64 LEU B 72 MET B 76 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000