HEADER ELECTRON TRANSPORT 23-MAY-98 1BFY TITLE SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM PASTEURIANUM RUBREDOXIN, TITLE 2 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, PARAMAGNETISM, KEYWDS 2 NUCLEAR RELAXATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.BERTINI,D.M.KURTZ JUNIOR,M.K.EIDSNESS,G.LIU,C.LUCHINAT,A.ROSATO, AUTHOR 2 R.A.SCOTT REVDAT 4 22-MAY-24 1BFY 1 REMARK REVDAT 3 16-FEB-22 1BFY 1 REMARK LINK 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,C.LUCHINAT, JRNL AUTH 2 A.ROSATO,R.A.SCOTT JRNL TITL SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM PASTEURIANUM JRNL TITL 2 RUBREDOXIN JRNL REF J.BIOL.INORG.CHEM. V. 3 401 1998 JRNL REFN ISSN 0949-8257 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 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 100 THE DEPOSITION ID IS D_1000171708. 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-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 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 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 REMARK 500 THIS ENTRY HAS 116 RAMACHANDRAN OUTLIERS. 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 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 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 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 SG CYS A 6 FE FE A 55 1555 1555 2.30 LINK SG CYS A 9 FE FE A 55 1555 1555 2.23 LINK SG CYS A 39 FE FE A 55 1555 1555 2.25 LINK SG CYS A 42 FE FE A 55 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 MODEL 1