Header list of 1dfd.pdb file
Complete list - b 16 2 Bytes
HEADER ELECTRON TRANSPORT 01-DEC-97 1DFD
TITLE OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, 19 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FERREDOXIN I;
COMPND 3 CHAIN: A;
COMPND 4 OTHER_DETAILS: OXIDIZED
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO AFRICANUS;
SOURCE 3 ORGANISM_TAXID: 873;
SOURCE 4 STRAIN: BENGHAZI
KEYWDS ELECTRON TRANSPORT, OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I,
KEYWDS 2 ELECTRON-TRANSFER PROTEIN, 4FE-4S CLUSTER
EXPDTA SOLUTION NMR
NUMMDL 19
AUTHOR S.L.DAVY,M.J.OSBORNE,G.R.MOORE
REVDAT 4 16-FEB-22 1DFD 1 REMARK LINK
REVDAT 3 24-MAR-09 1DFD 1 ATOM CONECT
REVDAT 2 24-FEB-09 1DFD 1 VERSN
REVDAT 1 13-JAN-99 1DFD 0
JRNL AUTH S.L.DAVY,M.J.OSBORNE,G.R.MOORE
JRNL TITL DETERMINATION OF THE STRUCTURE OF OXIDISED DESULFOVIBRIO
JRNL TITL 2 AFRICANUS FERREDOXIN I BY 1H NMR SPECTROSCOPY AND COMPARISON
JRNL TITL 3 OF ITS SOLUTION STRUCTURE WITH ITS CRYSTAL STRUCTURE.
JRNL REF J.MOL.BIOL. V. 277 683 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9533888
JRNL DOI 10.1006/JMBI.1998.1631
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.843
REMARK 3 AUTHORS : GUNTERT,WUTHRICH
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DFD 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_1000172765.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.2
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 90%H2O/10%D2O, 99.9%D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; TOCSY; NOESY; 1D NOE
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : JEOL GX-400; JEOL A-500; BRUKER
REMARK 210 AMX500 AND AMX600; VARIAN UNITY
REMARK 210 INOVA 600
REMARK 210 SPECTROMETER MANUFACTURER : JEOL; BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DIANA 2.5, X-PLOR 3.843
REMARK 210 METHOD USED : DISTANCE GEOMETRY, DG-SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 75
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19
REMARK 210 CONFORMERS, SELECTION CRITERIA : GOOD COVALENT GEOMETRY, LEAST
REMARK 210 EXPERIMENTAL RESTRAINTS
REMARK 210 VIOLATIONS (NOE<0.5, DIHEDRAL
REMARK 210 ANGLES<5), LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9
REMARK 210
REMARK 210 REMARK: THE STRUCTURES WERE OBTAINED USING 1H-1H 2D NMR
REMARK 210 EXPERIMENTS (DQF-COSY, TOCSY, NOESY). ADDITIONALLY 1D NOE
REMARK 210 EXPERIMENTS PROVIDED INFORMATION ON THE REGIONS OF THE PROTEIN
REMARK 210 CLOSE TO THE PARAMAGNETIC 4FE-4S CLUSTER.
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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-19
REMARK 470 RES CSSEQI ATOMS
REMARK 470 GLU A 64 O
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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 O ASP A 38 H GLY A 41 1.50
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 3 -156.47 -101.19
REMARK 500 1 PHE A 4 -167.39 179.78
REMARK 500 1 TYR A 5 -166.79 173.50
REMARK 500 1 ASP A 7 68.57 -106.76
REMARK 500 1 GLN A 8 -15.59 -47.72
REMARK 500 1 ILE A 12 -143.22 -88.78
REMARK 500 1 ALA A 13 52.92 -107.56
REMARK 500 1 ALA A 21 63.64 -174.43
REMARK 500 1 ALA A 26 126.31 -173.57
REMARK 500 1 GLU A 32 34.53 34.66
REMARK 500 1 VAL A 36 68.44 -67.51
REMARK 500 1 LYS A 37 -19.24 -49.95
REMARK 500 1 ASP A 38 99.72 -165.95
REMARK 500 1 THR A 53 -160.23 -59.98
REMARK 500 1 CYS A 54 144.63 66.74
REMARK 500 1 GLN A 57 -73.31 65.08
REMARK 500 2 ARG A 2 37.85 79.00
REMARK 500 2 LYS A 3 -154.37 -99.25
REMARK 500 2 PHE A 4 176.38 176.39
REMARK 500 2 TYR A 5 -157.11 175.66
REMARK 500 2 GLN A 8 40.08 -64.67
REMARK 500 2 ALA A 13 -29.90 164.40
REMARK 500 2 CYS A 14 154.80 -49.16
REMARK 500 2 ALA A 21 67.55 -179.30
REMARK 500 2 GLU A 32 42.41 27.91
REMARK 500 2 VAL A 36 67.90 -67.77
REMARK 500 2 ASP A 38 92.33 -166.17
REMARK 500 2 THR A 53 36.12 -97.15
REMARK 500 2 GLN A 57 86.71 42.39
REMARK 500 3 LYS A 3 -153.41 -96.82
REMARK 500 3 PHE A 4 176.87 168.59
REMARK 500 3 TYR A 5 -174.20 178.52
REMARK 500 3 GLN A 8 42.30 -63.24
REMARK 500 3 ALA A 13 32.78 79.76
REMARK 500 3 SER A 16 -82.64 -43.78
REMARK 500 3 ALA A 21 65.92 177.84
REMARK 500 3 GLU A 32 36.23 34.35
REMARK 500 3 ALA A 42 126.65 -179.66
REMARK 500 3 PRO A 55 -72.38 -76.35
REMARK 500 3 GLN A 57 -64.57 71.90
REMARK 500 4 LYS A 3 -163.25 -101.55
REMARK 500 4 PHE A 4 -174.33 167.98
REMARK 500 4 TYR A 5 -172.63 176.18
REMARK 500 4 GLN A 8 48.24 -66.22
REMARK 500 4 ALA A 13 70.85 76.53
REMARK 500 4 GLU A 15 -1.65 76.29
REMARK 500 4 ALA A 21 59.95 -177.54
REMARK 500 4 ALA A 26 119.57 -164.48
REMARK 500 4 GLU A 32 42.73 28.73
REMARK 500 4 ALA A 42 103.91 -160.04
REMARK 500
REMARK 500 THIS ENTRY HAS 227 RAMACHANDRAN OUTLIERS.
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 ARG A 2 0.09 SIDE CHAIN
REMARK 500 2 ARG A 2 0.30 SIDE CHAIN
REMARK 500 3 ARG A 2 0.29 SIDE CHAIN
REMARK 500 4 ARG A 2 0.30 SIDE CHAIN
REMARK 500 5 ARG A 2 0.30 SIDE CHAIN
REMARK 500 6 ARG A 2 0.32 SIDE CHAIN
REMARK 500 7 ARG A 2 0.30 SIDE CHAIN
REMARK 500 8 ARG A 2 0.24 SIDE CHAIN
REMARK 500 9 ARG A 2 0.16 SIDE CHAIN
REMARK 500 10 ARG A 2 0.20 SIDE CHAIN
REMARK 500 11 ARG A 2 0.28 SIDE CHAIN
REMARK 500 12 ARG A 2 0.31 SIDE CHAIN
REMARK 500 13 ARG A 2 0.32 SIDE CHAIN
REMARK 500 14 ARG A 2 0.24 SIDE CHAIN
REMARK 500 15 ARG A 2 0.28 SIDE CHAIN
REMARK 500 16 ARG A 2 0.30 SIDE CHAIN
REMARK 500 18 ARG A 2 0.27 SIDE CHAIN
REMARK 500 19 ARG A 2 0.23 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 SF4 A 65 FE1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 11 SG
REMARK 620 2 SF4 A 65 S2 105.3
REMARK 620 3 SF4 A 65 S3 113.7 107.7
REMARK 620 4 SF4 A 65 S4 115.6 106.1 107.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 65 FE4
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 14 SG
REMARK 620 2 SF4 A 65 S1 100.3
REMARK 620 3 SF4 A 65 S2 138.2 98.2
REMARK 620 4 SF4 A 65 S3 111.6 101.3 101.0
REMARK 620 5 CYS A 14 O 87.9 134.3 53.1 117.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 65 FE3
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 17 SG
REMARK 620 2 SF4 A 65 S1 102.1
REMARK 620 3 SF4 A 65 S2 114.6 107.6
REMARK 620 4 SF4 A 65 S4 126.6 105.0 99.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 65 FE2
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 54 SG
REMARK 620 2 SF4 A 65 S1 114.7
REMARK 620 3 SF4 A 65 S3 108.3 104.0
REMARK 620 4 SF4 A 65 S4 124.3 103.6 99.2
REMARK 620 N 1 2 3
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 65
DBREF 1DFD A 1 64 UNP P00210 FER1_DESAF 1 64
SEQRES 1 A 64 ALA ARG LYS PHE TYR VAL ASP GLN ASP GLU CYS ILE ALA
SEQRES 2 A 64 CYS GLU SER CYS VAL GLU ILE ALA PRO GLY ALA PHE ALA
SEQRES 3 A 64 MET ASP PRO GLU ILE GLU LYS ALA TYR VAL LYS ASP VAL
SEQRES 4 A 64 GLU GLY ALA SER GLN GLU GLU VAL GLU GLU ALA MET ASP
SEQRES 5 A 64 THR CYS PRO VAL GLN CYS ILE HIS TRP GLU ASP GLU
HET SF4 A 65 8
HETNAM SF4 IRON/SULFUR CLUSTER
FORMUL 2 SF4 FE4 S4
HELIX 1 1 GLN A 8 GLU A 10 5 3
HELIX 2 2 SER A 16 ALA A 21 1 6
HELIX 3 3 GLN A 44 ASP A 52 1 9
SHEET 1 A 2 ARG A 2 VAL A 6 0
SHEET 2 A 2 ILE A 59 ASP A 63 -1 N GLU A 62 O LYS A 3
SHEET 1 B 2 PHE A 25 ASP A 28 0
SHEET 2 B 2 LYS A 33 VAL A 36 -1 N TYR A 35 O ALA A 26
LINK SG CYS A 11 FE1 SF4 A 65 1555 1555 2.18
LINK SG CYS A 14 FE4 SF4 A 65 1555 1555 2.18
LINK O CYS A 14 FE4 SF4 A 65 1555 1555 2.56
LINK SG CYS A 17 FE3 SF4 A 65 1555 1555 2.18
LINK SG CYS A 54 FE2 SF4 A 65 1555 1555 2.18
SITE 1 AC1 7 CYS A 11 ILE A 12 CYS A 14 CYS A 17
SITE 2 AC1 7 PHE A 25 ALA A 34 CYS A 54
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
Complete list - b 16 2 Bytes