10 20 30 40 50 60 70 80 1BFY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 23-MAY-98 1BFY
TITLE SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM PASTEURIANUM TITLE 2 RUBREDOXIN, NMR, 20 STRUCTURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.18.1.1; COMPND 5 OTHER_DETAILS: REDUCED CLOSTRIDIUM PASTEURIANUM RUBREDOXIN
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PASTEURIANUM; SOURCE 3 ORGANISM_TAXID: 1501
KEYWDS ELECTRON TRANSPORT, RUBREDOXIN, SOLUTION STRUCTURE, KEYWDS 2 PARAMAGNETISM, NUCLEAR RELAXATION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR I.BERTINI,D.M.KURTZ JUNIOR,M.K.EIDSNESS,G.LIU,C.LUCHINAT, AUTHOR 2 A.ROSATO,R.A.SCOTT
REVDAT 2 24-FEB-09 1BFY 1 VERSN REVDAT 1 25-MAY-99 1BFY 0
JRNL AUTH I.BERTINI,D.M.KURTZ JUNIOR,M.K.EIDSNESS,G.LIU, JRNL AUTH 2 C.LUCHINAT,A.ROSATO,R.A.SCOTT JRNL TITL SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM JRNL TITL 2 PASTEURIANUM RUBREDOXIN JRNL REF J.BIOL.INORG.CHEM. V. 3 401 1998 JRNL REFN ISSN 0949-8257
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.4 REMARK 3 AUTHORS : GUNTERT,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1BFY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.1 M REMARK 210 PRESSURE : NORMAL REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, DQF-COSY, IR- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE800, AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BRUKER XWINNMR XWINNMR REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D NMR SPECTROSCOPY.
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 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 9 CYS A 42 CB - CA - C ANGL. DEV. = 8.3 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 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 LYS A 2 167.41 58.72 REMARK 500 1 CYS A 6 -97.56 -68.77 REMARK 500 1 THR A 7 -41.65 -172.95 REMARK 500 1 VAL A 8 -38.62 -147.79 REMARK 500 1 VAL A 44 -51.85 -145.46 REMARK 500 2 CYS A 6 -112.08 -74.84 REMARK 500 2 THR A 7 -158.20 -160.18 REMARK 500 2 CYS A 9 -55.85 -153.19 REMARK 500 2 CYS A 39 148.55 -34.57 REMARK 500 2 ASP A 47 -68.53 54.67 REMARK 500 3 CYS A 6 94.72 -58.91 REMARK 500 3 TYR A 11 66.13 -150.82 REMARK 500 3 ILE A 12 125.19 -37.79 REMARK 500 3 CYS A 39 144.02 -39.65 REMARK 500 3 LEU A 41 35.87 -149.32 REMARK 500 3 CYS A 42 -47.41 -131.19 REMARK 500 3 ASP A 47 85.83 21.11 REMARK 500 3 GLN A 48 150.66 75.20 REMARK 500 3 PHE A 49 109.44 -171.02 REMARK 500 4 LYS A 2 162.00 62.54 REMARK 500 4 CYS A 6 47.45 -77.56 REMARK 500 4 THR A 7 -124.27 43.39 REMARK 500 4 CYS A 9 -70.04 -133.00 REMARK 500 4 TYR A 11 -57.63 -131.91 REMARK 500 4 ILE A 12 119.15 75.17 REMARK 500 4 VAL A 44 -149.39 48.07 REMARK 500 4 ASP A 47 -63.59 -158.43 REMARK 500 5 LYS A 2 168.36 60.15 REMARK 500 5 VAL A 8 -65.15 -123.34 REMARK 500 5 CYS A 9 -60.53 -94.56 REMARK 500 5 VAL A 44 123.35 78.84 REMARK 500 5 LYS A 46 74.05 53.87 REMARK 500 5 ASP A 47 -69.67 -152.59 REMARK 500 6 THR A 7 81.02 -69.28 REMARK 500 6 VAL A 8 -74.88 66.98 REMARK 500 6 CYS A 9 -122.68 43.05 REMARK 500 6 ASP A 19 63.94 -151.87 REMARK 500 6 CYS A 42 -68.19 -142.67 REMARK 500 6 LYS A 46 33.89 -148.55 REMARK 500 7 LYS A 2 171.60 62.18 REMARK 500 7 VAL A 8 24.22 -140.50 REMARK 500 7 TYR A 11 65.27 21.00 REMARK 500 7 LEU A 41 -62.31 68.80 REMARK 500 8 LYS A 2 173.38 54.64 REMARK 500 8 VAL A 8 16.20 -148.57 REMARK 500 8 ILE A 12 128.06 71.32 REMARK 500 8 LYS A 46 -88.02 62.38 REMARK 500 8 ASP A 47 -72.48 46.83 REMARK 500 9 LYS A 2 167.82 64.04 REMARK 500 9 THR A 7 -94.41 53.84 REMARK 500 9 TYR A 11 -57.76 -134.88 REMARK 500 9 ILE A 12 121.25 75.22 REMARK 500 9 VAL A 44 -73.23 -143.58 REMARK 500 9 ASP A 47 -93.74 30.09 REMARK 500 9 GLN A 48 64.84 -150.34 REMARK 500 9 PHE A 49 156.12 -45.72 REMARK 500 10 LYS A 2 174.94 57.79 REMARK 500 10 THR A 7 -74.18 -76.40 REMARK 500 10 VAL A 44 -71.20 -99.50 REMARK 500 10 ASP A 47 -82.93 -163.54 REMARK 500 10 PHE A 49 92.43 49.32 REMARK 500 11 LYS A 2 167.47 62.60 REMARK 500 11 THR A 7 -82.36 -25.84 REMARK 500 11 CYS A 9 -78.09 -141.09 REMARK 500 11 LEU A 41 43.54 70.19 REMARK 500 11 LYS A 46 78.32 58.57 REMARK 500 11 ASP A 47 -99.68 -153.81 REMARK 500 12 LYS A 2 170.29 59.73 REMARK 500 12 THR A 7 -72.37 65.64 REMARK 500 12 TYR A 11 63.88 22.19 REMARK 500 12 PRO A 40 95.81 -69.60 REMARK 500 12 LEU A 41 59.11 85.42 REMARK 500 12 CYS A 42 -94.67 -147.22 REMARK 500 12 ASP A 47 -65.84 -138.85 REMARK 500 13 LYS A 2 165.33 62.47 REMARK 500 13 CYS A 6 -121.01 -81.37 REMARK 500 13 THR A 7 -46.08 -160.49 REMARK 500 13 VAL A 8 -66.75 -104.65 REMARK 500 13 TYR A 11 87.21 -65.76 REMARK 500 13 ASP A 47 -94.42 29.26 REMARK 500 13 PHE A 49 156.26 -47.73 REMARK 500 14 LYS A 2 162.34 66.09 REMARK 500 14 THR A 7 -76.18 -41.60 REMARK 500 14 VAL A 8 48.50 -99.70 REMARK 500 14 CYS A 9 -60.95 -160.95 REMARK 500 14 LYS A 46 101.78 59.50 REMARK 500 14 ASP A 47 -75.73 -138.80 REMARK 500 14 GLN A 48 55.34 -144.69 REMARK 500 15 THR A 7 -99.26 -82.29 REMARK 500 15 GLN A 48 -38.66 -171.92 REMARK 500 16 VAL A 8 -60.54 -132.50 REMARK 500 16 CYS A 9 -89.31 -95.92 REMARK 500 16 CYS A 42 -57.61 -147.76 REMARK 500 16 GLN A 48 -30.06 -179.37 REMARK 500 16 GLU A 53 82.13 -69.00 REMARK 500 17 LYS A 2 174.82 55.83 REMARK 500 17 VAL A 8 35.91 -153.35 REMARK 500 17 CYS A 9 -65.25 -121.79 REMARK 500 17 CYS A 42 -97.83 -125.65 REMARK 500 17 VAL A 44 -173.20 76.94 REMARK 500 17 ASP A 47 -75.49 -159.45 REMARK 500 17 PHE A 49 173.47 53.15 REMARK 500 18 LYS A 2 164.38 66.32 REMARK 500 18 THR A 7 -62.46 76.14 REMARK 500 18 VAL A 8 43.72 -78.79 REMARK 500 18 CYS A 9 -102.49 177.05 REMARK 500 18 ILE A 12 110.73 79.84 REMARK 500 18 LEU A 41 51.50 -150.80 REMARK 500 18 CYS A 42 -64.68 -142.84 REMARK 500 18 VAL A 44 -83.65 61.77 REMARK 500 18 GLN A 48 47.02 36.93 REMARK 500 19 LYS A 2 165.76 62.09 REMARK 500 19 VAL A 8 -32.74 -160.98 REMARK 500 19 CYS A 42 -66.79 -162.90 REMARK 500 20 ILE A 12 113.01 69.64 REMARK 500 20 ASP A 47 -63.24 69.59 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 GLU A 53 GLU A 54 6 149.72 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 A 4 0.09 SIDE_CHAIN REMARK 500 1 TYR A 13 0.08 SIDE_CHAIN REMARK 500 2 TYR A 11 0.10 SIDE_CHAIN REMARK 500 2 TYR A 13 0.07 SIDE_CHAIN REMARK 500 3 TYR A 4 0.08 SIDE_CHAIN REMARK 500 3 TYR A 13 0.07 SIDE_CHAIN REMARK 500 4 TYR A 4 0.09 SIDE_CHAIN REMARK 500 4 TYR A 13 0.08 SIDE_CHAIN REMARK 500 5 TYR A 13 0.08 SIDE_CHAIN REMARK 500 6 TYR A 13 0.08 SIDE_CHAIN REMARK 500 7 TYR A 4 0.12 SIDE_CHAIN REMARK 500 7 TYR A 13 0.08 SIDE_CHAIN REMARK 500 10 TYR A 13 0.09 SIDE_CHAIN REMARK 500 11 TYR A 4 0.09 SIDE_CHAIN REMARK 500 12 TYR A 13 0.09 SIDE_CHAIN REMARK 500 12 PHE A 30 0.09 SIDE_CHAIN REMARK 500 13 TYR A 4 0.12 SIDE_CHAIN REMARK 500 14 TYR A 13 0.07 SIDE_CHAIN REMARK 500 16 TYR A 4 0.10 SIDE_CHAIN REMARK 500 16 TYR A 13 0.08 SIDE_CHAIN REMARK 500 16 PHE A 30 0.08 SIDE_CHAIN REMARK 500 17 TYR A 4 0.11 SIDE_CHAIN REMARK 500 17 TYR A 13 0.08 SIDE_CHAIN REMARK 500 18 TYR A 4 0.10 SIDE_CHAIN REMARK 500 18 TYR A 13 0.09 SIDE_CHAIN REMARK 500 19 TYR A 13 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 MET A 1 124.5 ALPHA-CARBON REMARK 500 4 MET A 1 122.3 ALPHA-CARBON REMARK 500 5 MET A 1 124.1 ALPHA-CARBON REMARK 500 7 MET A 1 125.6 ALPHA-CARBON REMARK 500 8 MET A 1 126.3 ALPHA-CARBON REMARK 500 9 MET A 1 123.1 ALPHA-CARBON REMARK 500 10 MET A 1 122.4 ALPHA-CARBON REMARK 500 11 MET A 1 125.1 ALPHA-CARBON REMARK 500 12 MET A 1 124.2 ALPHA-CARBON REMARK 500 13 MET A 1 123.6 ALPHA-CARBON REMARK 500 14 MET A 1 123.6 ALPHA-CARBON REMARK 500 17 MET A 1 121.3 ALPHA-CARBON REMARK 500 18 MET A 1 123.1 ALPHA-CARBON REMARK 500 19 MET A 1 126.3 ALPHA-CARBON 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 1 FE A 55 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 92.5 REMARK 620 3 CYS A 39 SG 100.5 121.0 REMARK 620 4 CYS A 42 SG 125.0 106.2 111.7 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FEB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: IRON BINDING SITE. REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 55
DBREF 1BFY A 1 54 UNP P00268 RUBR_CLOPA 1 54
SEQRES 1 A 54 MET LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE TYR SEQRES 2 A 54 ASN PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN PRO SEQRES 3 A 54 GLY THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL CYS SEQRES 4 A 54 PRO LEU CYS GLY VAL GLY LYS ASP GLN PHE GLU GLU VAL SEQRES 5 A 54 GLU GLU
HET FE A 55 1
HETNAM FE FE (III) ION
FORMUL 2 FE FE 3+
SHEET 1 A 2 LYS A 3 TYR A 4 0 SHEET 2 A 2 GLU A 51 VAL A 52 -1 N VAL A 52 O LYS A 3
LINK FE FE A 55 SG CYS A 6 1555 1555 2.30 LINK FE FE A 55 SG CYS A 9 1555 1555 2.23 LINK FE FE A 55 SG CYS A 39 1555 1555 2.25 LINK FE FE A 55 SG CYS A 42 1555 1555 2.25
SITE 1 FEB 4 CYS A 6 CYS A 9 CYS A 39 CYS A 42 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 39 CYS A 42
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