HEADER ELECTRON TRANSFER (IRON-SULFUR PROTEIN) 17-OCT-96 1CJN OBSLTE 15-MAY-97 1CJN 2CJN TITLE STRUCTURE OF FERREDOXIN, NMR, MINIMIZED STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN; COMPND 3 CHAIN: NULL; COMPND 4 OTHER_DETAILS: 2FE-2S SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS; SOURCE 3 ORGANISM_COMMON: CYANOBACTERIUM KEYWDS FERREDOXIN, ELECTRON TRANSFER (IRON-SULFUR PROTEIN) EXPDTA NMR AUTHOR H.HATANAKA,R.TANIMURA,S.KATOH,F.INAGAKI REVDAT 1 11-JAN-97 1CJN 0 JRNL AUTH H.HATANAKA,R.TANIMURA,S.KATOH,F.INAGAKI JRNL TITL SOLUTION STRUCTURE OF FERREDOXIN FROM THERMOPHILIC JRNL TITL 2 CYANOBACTERIUM SYNECHOCOCCUS ELONGATUS AND ITS JRNL TITL 3 THERMOSTABILITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : .PROR REMARK 3 AUTHORS : BRUNGER NUMBER OF NON-HYDROGEN ATOMS USED IN REMARK 3 REFINEMENT. PROTEIN ATOMS : 1458 NUCLEIC ACID REMARK 3 ATOMS : 0 HETEROGEN ATOMS : 0 SOLVENT ATOMS : 0 REMARK 3 PARAMETER FILE 1 : PARALLHDG REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION. THE METHOD REMARK 3 USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID REMARK 3 DISTANCE GEOMETRY - DYNAMICAL SIMULATED ANNEALING METHOD REMARK 3 (NILGES ET AL. (1988) FEBS LETT. 229, 317-324) USING THE REMARK 3 PROGRAM *DSPACE* (HARE RESEARCH, VER 4.0) AND THE PROGRAM *X- REMARK 3 PLOR* (MOLECULAR SIMULATIONS, VER 2.1, A.T.BRUNGER, YALE REMARK 3 UNIVERSITY, NEW HAVEN, CT 06511). STRUCTURAL STATISTICS - RMS REMARK 3 DEVIATION FROM EXPERIMENTAL RESTRAINTS RESTRAINT TYPE NUMBER REMARK 3 RMS (ANGSTROMS) OF RESTRAINTS MEAN MODEL MODEL 1-10 DISTANCE REMARK 3 RESTRAINTS *(1)* ALL 1171 0.064 0.067 (0.002) DISULFIDE BOND 0 REMARK 3 HYDROGEN BOND 0 DIHEDRAL RESTRAINTS *(2)* ALL 0 - - (DEGS) REMARK 3 POTENTIAL ENERGY TERMS TYPE ENERGY (KCAL/MOL) MEAN MODEL MODEL REMARK 3 1-10 F(NOE) *(3)* 241.4 265.5 (15.2) F(TOR) *(4)* - - F(REPEL) REMARK 3 *(5)* 199.8 211.6 (9.7) LENNARD-JONES VAN DER WAALS ENERGY REMARK 3 (E(L-J)) CALCULATED USING THE *CHARMM* EMPIRICAL ENERGY REMARK 3 FUNCTION IS -411 KCAL/MOL (MEAN MODEL), AND -416(10) KCAL/MOL REMARK 3 (MODEL 1-10). IT IS NOT INCLUDED IN THE TARGET FUNCTION FOR REMARK 3 SIMULATED ANNEALING. DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* REMARK 3 TYPE TOTAL NUMBER RMS DEVIATION MEAN MODEL MODEL 1-10 BONDS REMARK 3 1468 0.006 0.007 (0.001) (ANGSTROMS) ANGLES 2653 2.065 2.42 REMARK 3 (0.011) (DEGREES) IMPROPERS 575 1.279 1.45 (0.026) (DEGREES) REMARK 3 NOTES. *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL REMARK 3 RESTRAINTS IS CALCULATED WITH RESPECT TO THE UPPER AND LOWER REMARK 3 LIMITS OF THE DISTANCE RESTRAINTS. THE UPPER LIMITS WERE REMARK 3 DERIVED FROM NOE CROSSPEAK INTENSITIES ON THE BASIS OF A REMARK 3 RELATION OF (DISTANCE) = K * (NOE INTENSITY)^(-1/6) + 0.5 REMARK 3 (ANGSTROMS). THE VALUE OF K WAS DETERMINED FROM THE KNOWN REMARK 3 STANDARD DISTANCES. THE LOWER LIMITS WERE SET TO 1.8 REMARK 3 ANGSTROMS. THE NUMBER OF VIOLATIONS GREATER THAN 0.5 ANGSTROMS REMARK 3 IS 3 (MAX 0.54 ANGSTROMS FOR MEAN MODEL AND 0-2 (MAX 0.56 REMARK 3 ANGSTROMS) FOR MODEL 1-10. *(2)* THE RMS DEVIATION FROM THE REMARK 3 EXPERIMENTAL RESTRAINTS IS CALCULATED WITH RESPECT TO THE REMARK 3 UPPER AND LOWER LIMITS OF THE DIHEDRAL RESTRAINTS. NO DIHEDRAL REMARK 3 CONSTRAINTS WERE USED IN THIS CALCULATION. *(3)* THE VALUES OF REMARK 3 THE SQUARE-WELL NOE POTENTIAL WITH A FORCE CONSTANT OF 50 REMARK 3 KCAL/MOL/ANGSTROM**2. *(4)* THE VALUES OF F(TOR) ARE REMARK 3 CALCULATED WITH A FORCE CONSTANT OF 50 KCAL/MOL/RAD**2. F(TOR) REMARK 3 IS A SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO RESTRICT REMARK 3 THE RANGES OF TORSION ANGLES. *(5)* THE VALUE OF THE VAN DER REMARK 3 WAALS REPULSION TERM F(REPEL) IS CALCULATED WITH A FORCE REMARK 3 CONSTANT OF 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE VAN REMARK 3 DER WAALS RADII SET TO 0.8 TIMES THE STANDARD VALUES USED IN REMARK 3 THE *CHARMM* EMPIRICAL ENERGY FUNCTION. NBXMOD=-4 *(6)* THE REMARK 3 IMPROPER TERMS SERVE TO MAINTAIN PLANARITY AND APPROPRIATE REMARK 3 CHIRALITY. THE RESTRAINTS FOR THE DISULFIDE BRIDGES WERE REMARK 3 INCLUDED IN THE BOND AND ANGLES TERMS JUST BEFORE THE COOLING REMARK 3 STAGE OF THE *X-PLOR* PROTOCOL. REMARK 4 REMARK 4 1CJN COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 THE MEAN STRUCTURE WAS OBTAINED BY AVERAGING THE REMARK 6 COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE REMARK 6 RESULTING COORDINATES TO FURTHER RESTRAINED MINIMIZATION. REMARK 7 REMARK 7 HYDROGEN ATOMS IN THIS ENTRY HAVE BEEN ASSIGNED NAMES REMARK 7 CONSISTENT WITH THE RECOMMENDATIONS OF THE IUPAC-IUB REMARK 7 COMMISSION ON BIOCHEMICAL NOMENCLATURE (SEE, E.G., J.MOL. REMARK 7 BIOL. 52, 1-17 (1970)). THE PROTEIN DATA BANK HAS FOLLOWED REMARK 7 RULE 4.4 OF THE RECOMMENDATIONS WITH THE FOLLOWING REMARK 7 MODIFICATION - WHEN MORE THAN ONE HYDROGEN ATOM IS BONDED REMARK 7 TO A SINGLE NON-HYDROGEN ATOM, THE HYDROGEN ATOM NUMBER REMARK 7 DESIGNATION IS GIVEN AS THE FIRST CHARACTER OF THE ATOM REMARK 7 NAME RATHER THAN AS THE LAST CHARACTER (E.G. H*BETA*1 IS REMARK 7 DENOTED AS 1HB). REMARK 8 REMARK 8 THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE REMARK 8 THE AVERAGE OF THE RMS DIFFERENCES (MEAN MODEL) PER ATOM REMARK 8 BETWEEN THE INDIVIDUAL STRUCTURES AND THE MEAN STRUCTURE REMARK 8 STRUCTURE (IN ANGSTROMS). THE RMS DIFFERENCES WERE REMARK 8 OBTAINED FOR A GIVEN STRUCTURE AFTER THE BACKBONE ATOMS OF REMARK 8 RESIDUES 1 - 97 WERE FITTED TO THE BACKBONE OF THE MEAN REMARK 8 STRUCTURE, AND THEN AVERAGED. REMARK 9 REMARK 9 THE RESONANCES OF PROTONS CLOSE TO THE PARAMAGNETIC REMARK 9 IRON-SULFUR CENTER WERE BROADENED. THEREFORE THE AUTHORS REMARK 9 CALCULATED INTERPROTON DISTANCES FROM 1.8 TO 5 ANGSTROMS REMARK 9 AMONG THE 19 RESIDUES, PRO 37 - ALA 49, SER 63 - PHE 64 REMARK 9 AND LEU 76 - VAL 79, WHERE THE RESONANCES OF HN OR HA REMARK 9 DISAPPEARED, ON THE TERTIARY STRUCTURE OF SPIRULINA REMARK 9 PLATENSIS FERREDOXIN (PDB ENTRY 3FXC). THEN ONLY THOSE REMARK 9 FROM ATOM PAIRS SEPARATED BY MORE THAN ONE RESIDUE WERE REMARK 9 USED AS THE UPPER LIMIT CONSTRAINTS (225). REMARK 10 REMARK 10 THE IRON-SULFUR CLUSTER HAS BEEN REPLACED BY FOUR REMARK 10 HYDROGENS. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, TOCSY, NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : ALPHA-600 REMARK 210 SPECTROMETER MANUFACTURER : JEOL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : F(NOE) + F(REPEL) REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NMR DATA WERE COLLECTED IN H2O IN 0.010 M SODIUM REMARK 210 PHOSPHATE BUFFER PH 7.2 CONTAINING 10 PERCENT D2O AND 0.050 M REMARK 210 SODIUM CHLORIDE AT 20 DEGREES CELSIUS. 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER 63 CA - CB - OG ANGL. DEV. =-39.2 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 THIS ENTRY IS THE MINIMIZED STRUCTURE. THE 10 CONFORMERS REMARK 900 USED TO GENERATE THIS MINIMIZED STRUCTURE CAN BE FOUND IN REMARK 900 PDB ENTRY 1CJO. DBREF 1CJN 1 97 UNP P00256 FER_SYNEL 1 97 SEQRES 1 97 ALA THR TYR LYS VAL THR LEU VAL ARG PRO ASP GLY SER SEQRES 2 97 GLU THR THR ILE ASP VAL PRO GLU ASP GLU TYR ILE LEU SEQRES 3 97 ASP VAL ALA GLU GLU GLN GLY LEU ASP LEU PRO PHE SER SEQRES 4 97 CYS ARG ALA GLY ALA CYS SER THR CYS ALA GLY LYS LEU SEQRES 5 97 LEU GLU GLY GLU VAL ASP GLN SER ASP GLN SER PHE LEU SEQRES 6 97 ASP ASP ASP GLN ILE GLU LYS GLY PHE VAL LEU THR CYS SEQRES 7 97 VAL ALA TYR PRO ARG SER ASP CYS LYS ILE LEU THR ASN SEQRES 8 97 GLN GLU GLU GLU LEU TYR HELIX 1 A ILE 25 GLN 32 1 8 HELIX 2 B ASP 67 LYS 72 1 6 HELIX 3 C GLU 94 TYR 97 1 4 SHEET 1 A 4 SER 13 GLU 21 0 SHEET 2 A 4 THR 2 PRO 10 -1 O LEU 7 N THR 15 SHEET 3 A 4 SER 84 THR 90 1 O ILE 88 N VAL 8 SHEET 4 A 4 LYS 51 LEU 53 -1 O LYS 51 N LEU 89 SHEET 1 B 2 GLU 56 GLN 59 0 SHEET 2 B 2 ALA 80 ARG 83 -1 O TYR 81 N ASP 58 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