HEADER OXIDOREDUCTASE 16-NOV-15 5FNP TITLE HIGH RESOLUTION ZN CONTAINING IRON SULFUR CLUSTER REPAIR PROTEIN YTFE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: REGULATOR OF CELL MORPHOGENESIS AND NO SIGNALING, RCMNS, COMPND 5 YTFE; COMPND 6 EC: 1.7.2.5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS OXIDOREDUCTASE, NITRIC OXIDE, IRON-SULFUR CLUSTER REPAIR, DI-FE KEYWDS 2 CENTER. EXPDTA X-RAY DIFFRACTION AUTHOR F.-C.LO,C.-C.HSIEH,M.MAESTRE-REYNA,C.-Y.CHEN,T.-P.KO,Y.-C.HORNG,Y.- AUTHOR 2 C.LAI,Y.-W.CHIANG,C.-M.CHOU,C.-H.CHIANG,W.-N.HUANG,W.-F.LIAW REVDAT 4 10-JAN-24 5FNP 1 REMARK LINK REVDAT 3 13-JUL-16 5FNP 1 JRNL REVDAT 2 15-JUN-16 5FNP 1 JRNL REVDAT 1 27-APR-16 5FNP 0 JRNL AUTH F.-C.LO,C.-C.HSIEH,M.MAESTRE-REYNA,C.-Y.CHEN,T.-P.KO, JRNL AUTH 2 Y.-C.HORNG,Y.-C.LAI,Y.-W.CHIANG,C.-M.CHOU,C.-H.CHIANG, JRNL AUTH 3 W.-N.HUANG,W.-F.LIAW JRNL TITL CRYSTAL STRUCTURE OF THE REPAIR OF IRON CENTERS PROTEIN YTFE JRNL TITL 2 AND ITS INTERACTION WITH NO JRNL REF CHEMISTRY V. 22 9768 2016 JRNL REFN ISSN 0947-6539 JRNL PMID 27246459 JRNL DOI 10.1002/CHEM.201600990 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 48586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2561 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2864 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3282 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.84000 REMARK 3 B22 (A**2) : 1.84000 REMARK 3 B33 (A**2) : -3.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.418 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3390 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3192 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4601 ; 1.439 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7374 ; 1.174 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 436 ; 4.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;40.031 ;24.895 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 586 ;12.712 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 521 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3807 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 686 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1723 ; 1.709 ; 3.672 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1722 ; 1.709 ; 3.671 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2151 ; 2.659 ; 5.491 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1667 ; 2.577 ; 3.789 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 36.1940 -2.4950 41.0270 REMARK 3 T TENSOR REMARK 3 T11: 0.0213 T22: 0.0245 REMARK 3 T33: 0.1015 T12: 0.0096 REMARK 3 T13: 0.0013 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 0.2736 L22: 0.5262 REMARK 3 L33: 1.2122 L12: 0.3698 REMARK 3 L13: 0.3030 L23: 0.2795 REMARK 3 S TENSOR REMARK 3 S11: -0.0242 S12: -0.0696 S13: 0.0708 REMARK 3 S21: -0.0388 S22: -0.1016 S23: 0.0860 REMARK 3 S31: -0.0745 S32: -0.0440 S33: 0.1259 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 223 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6800 -1.2070 -10.0550 REMARK 3 T TENSOR REMARK 3 T11: 0.0721 T22: 0.0459 REMARK 3 T33: 0.0286 T12: -0.0304 REMARK 3 T13: -0.0238 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 0.3575 L22: 0.3239 REMARK 3 L33: 2.5051 L12: -0.2602 REMARK 3 L13: 0.3156 L23: -0.2988 REMARK 3 S TENSOR REMARK 3 S11: 0.0553 S12: 0.0004 S13: -0.0122 REMARK 3 S21: 0.0125 S22: -0.0794 S23: -0.0499 REMARK 3 S31: -0.2759 S32: 0.0371 S33: 0.0240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 5FNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1290065539. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5FNN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS/HCL PH 8.5 20% PEG8000 0.2 REMARK 280 M MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 49.22700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 49.22700 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.06900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.22700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.53450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.22700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 94.60350 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.22700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.22700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.06900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 49.22700 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 94.60350 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 49.22700 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 31.53450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 56 REMARK 465 LYS B 57 REMARK 465 LEU B 58 REMARK 465 ALA B 59 REMARK 465 GLU B 60 REMARK 465 GLN B 61 REMARK 465 PRO B 62 REMARK 465 ILE B 63 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 45 OE1 OE2 REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 LEU A 58 CG CD1 CD2 REMARK 470 GLN A 61 CG CD OE1 NE2 REMARK 470 PRO A 62 CG CD REMARK 470 ILE A 63 CG1 CG2 CD1 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 TYR B 3 CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 5 CG OD1 OD2 REMARK 470 GLN B 6 CG CD OE1 NE2 REMARK 470 GLU B 10 CG CD OE1 OE2 REMARK 470 LEU B 11 CG CD1 CD2 REMARK 470 ARG B 17 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 24 CG CD CE NZ REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 THR B 36 OG1 CG2 REMARK 470 ARG B 39 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 43 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 44 CD CE NZ REMARK 470 LEU B 46 CD1 CD2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 VAL B 48 CG1 CG2 REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 VAL B 50 CG1 CG2 REMARK 470 GLU B 52 CD OE1 OE2 REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 LYS B 132 CE NZ 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 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG B 88 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 88 NE - CZ - NH2 ANGL. DEV. = -4.8 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 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 ARG A 17 5.70 59.46 REMARK 500 ILE A 63 108.21 -58.60 REMARK 500 ILE A 136 -59.28 -127.66 REMARK 500 CYS A 184 -166.10 -110.72 REMARK 500 CYS A 184 -166.06 -110.76 REMARK 500 VAL A 211 -63.45 -125.36 REMARK 500 ARG B 17 5.95 59.22 REMARK 500 ILE B 136 -60.06 -126.74 REMARK 500 CYS B 184 -166.90 -111.23 REMARK 500 CYS B 184 -167.40 -110.69 REMARK 500 VAL B 211 -64.07 -125.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3029 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A3051 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A3052 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A3058 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A3061 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A3068 DISTANCE = 7.94 ANGSTROMS REMARK 525 HOH A3076 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A3079 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A3118 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B3017 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B3020 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH B3021 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH B3030 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH B3031 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH B3097 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B3172 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH B3173 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH B3174 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH B3176 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH B3177 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH B3178 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH B3180 DISTANCE = 8.10 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 OXO GROUP (OXO): U-OXO BRIDGE IN THE METAL CLUSTER 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 ZN A1222 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 84 NE2 REMARK 620 2 GLU A 133 OE1 89.7 REMARK 620 3 HIS A 204 NE2 91.3 171.0 REMARK 620 4 GLU A 208 OE2 119.1 97.2 90.1 REMARK 620 5 O A2118 O 121.6 86.9 85.0 119.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1221 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 NE2 REMARK 620 2 GLU A 133 OE2 90.5 REMARK 620 3 HIS A 160 NE2 93.4 122.3 REMARK 620 4 GLU A 208 OE1 175.9 88.2 84.0 REMARK 620 5 O A2118 O 92.3 110.8 126.5 91.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1222 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 84 NE2 REMARK 620 2 GLU B 133 OE1 88.4 REMARK 620 3 HIS B 204 NE2 91.7 171.9 REMARK 620 4 GLU B 208 OE2 117.8 96.5 90.6 REMARK 620 5 O B2097 O 122.8 87.6 85.6 119.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1221 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 129 NE2 REMARK 620 2 GLU B 133 OE2 90.3 REMARK 620 3 HIS B 160 NE2 92.9 123.2 REMARK 620 4 GLU B 208 OE1 175.5 87.5 85.0 REMARK 620 5 O B2097 O 92.9 108.7 127.6 91.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O A 2118 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O B 2097 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FNN RELATED DB: PDB REMARK 900 IRON AND SELENOMETHIONINE CONTAINING IRON SULFUR CLUSTER REPAIR REMARK 900 PROTEIN YTFE REMARK 900 RELATED ID: 5FNY RELATED DB: PDB REMARK 900 LOW SOLVENT CONTENT CRYSTAL FORM OF ZN CONTAINING IRON SULFUR REMARK 900 CLUSTER REPAIR PROTEIN YTFE REMARK 999 REMARK 999 SEQUENCE REMARK 999 OUR CONSTRUCT INCLUDED MUTATIONS ON C30 AND C31 TO A DBREF 5FNP A 1 220 UNP P69506 YTFE_ECOLI 1 220 DBREF 5FNP B 1 220 UNP P69506 YTFE_ECOLI 1 220 SEQADV 5FNP ALA A 30 UNP P69506 CYS 30 ENGINEERED MUTATION SEQADV 5FNP ALA A 31 UNP P69506 CYS 31 ENGINEERED MUTATION SEQADV 5FNP ALA B 30 UNP P69506 CYS 30 ENGINEERED MUTATION SEQADV 5FNP ALA B 31 UNP P69506 CYS 31 ENGINEERED MUTATION SEQRES 1 A 220 MET ALA TYR ARG ASP GLN PRO LEU GLY GLU LEU ALA LEU SEQRES 2 A 220 SER ILE PRO ARG ALA SER ALA LEU PHE ARG LYS TYR ASP SEQRES 3 A 220 MET ASP TYR ALA ALA GLY GLY LYS GLN THR LEU ALA ARG SEQRES 4 A 220 ALA ALA ALA ARG LYS GLU LEU ASP VAL GLU VAL ILE GLU SEQRES 5 A 220 ALA GLU LEU ALA LYS LEU ALA GLU GLN PRO ILE GLU LYS SEQRES 6 A 220 ASP TRP ARG SER ALA PRO LEU ALA GLU ILE ILE ASP HIS SEQRES 7 A 220 ILE ILE VAL ARG TYR HIS ASP ARG HIS ARG GLU GLN LEU SEQRES 8 A 220 PRO GLU LEU ILE LEU GLN ALA THR LYS VAL GLU ARG VAL SEQRES 9 A 220 HIS ALA ASP LYS PRO SER VAL PRO LYS GLY LEU THR LYS SEQRES 10 A 220 TYR LEU THR MET LEU HIS GLU GLU LEU SER SER HIS MET SEQRES 11 A 220 MET LYS GLU GLU GLN ILE LEU PHE PRO MET ILE LYS GLN SEQRES 12 A 220 GLY MET GLY SER GLN ALA MET GLY PRO ILE SER VAL MET SEQRES 13 A 220 GLU SER GLU HIS ASP GLU ALA GLY GLU LEU LEU GLU VAL SEQRES 14 A 220 ILE LYS HIS THR THR ASN ASN VAL THR PRO PRO PRO GLU SEQRES 15 A 220 ALA CYS THR THR TRP LYS ALA MET TYR ASN GLY ILE ASN SEQRES 16 A 220 GLU LEU ILE ASP ASP LEU MET ASP HIS ILE SER LEU GLU SEQRES 17 A 220 ASN ASN VAL LEU PHE PRO ARG ALA LEU ALA GLY GLU SEQRES 1 B 220 MET ALA TYR ARG ASP GLN PRO LEU GLY GLU LEU ALA LEU SEQRES 2 B 220 SER ILE PRO ARG ALA SER ALA LEU PHE ARG LYS TYR ASP SEQRES 3 B 220 MET ASP TYR ALA ALA GLY GLY LYS GLN THR LEU ALA ARG SEQRES 4 B 220 ALA ALA ALA ARG LYS GLU LEU ASP VAL GLU VAL ILE GLU SEQRES 5 B 220 ALA GLU LEU ALA LYS LEU ALA GLU GLN PRO ILE GLU LYS SEQRES 6 B 220 ASP TRP ARG SER ALA PRO LEU ALA GLU ILE ILE ASP HIS SEQRES 7 B 220 ILE ILE VAL ARG TYR HIS ASP ARG HIS ARG GLU GLN LEU SEQRES 8 B 220 PRO GLU LEU ILE LEU GLN ALA THR LYS VAL GLU ARG VAL SEQRES 9 B 220 HIS ALA ASP LYS PRO SER VAL PRO LYS GLY LEU THR LYS SEQRES 10 B 220 TYR LEU THR MET LEU HIS GLU GLU LEU SER SER HIS MET SEQRES 11 B 220 MET LYS GLU GLU GLN ILE LEU PHE PRO MET ILE LYS GLN SEQRES 12 B 220 GLY MET GLY SER GLN ALA MET GLY PRO ILE SER VAL MET SEQRES 13 B 220 GLU SER GLU HIS ASP GLU ALA GLY GLU LEU LEU GLU VAL SEQRES 14 B 220 ILE LYS HIS THR THR ASN ASN VAL THR PRO PRO PRO GLU SEQRES 15 B 220 ALA CYS THR THR TRP LYS ALA MET TYR ASN GLY ILE ASN SEQRES 16 B 220 GLU LEU ILE ASP ASP LEU MET ASP HIS ILE SER LEU GLU SEQRES 17 B 220 ASN ASN VAL LEU PHE PRO ARG ALA LEU ALA GLY GLU HET ZN A1221 1 HET ZN A1222 1 HET CL A1223 1 HET O A2118 1 HET ZN B1221 1 HET ZN B1222 1 HET CL B1223 1 HET O B2097 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM O OXYGEN ATOM FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CL 2(CL 1-) FORMUL 6 O 2(O) FORMUL 11 HOH *438(H2 O) HELIX 1 1 ALA A 2 GLN A 6 5 5 HELIX 2 2 PRO A 7 ILE A 15 1 9 HELIX 3 3 ARG A 17 TYR A 25 1 9 HELIX 4 4 THR A 36 LYS A 44 1 9 HELIX 5 5 ASP A 47 GLN A 61 1 15 HELIX 6 6 ASP A 66 ALA A 70 5 5 HELIX 7 7 PRO A 71 TYR A 83 1 13 HELIX 8 8 TYR A 83 HIS A 105 1 23 HELIX 9 9 GLY A 114 ILE A 136 1 23 HELIX 10 10 ILE A 136 GLN A 143 1 8 HELIX 11 11 MET A 145 GLN A 148 5 4 HELIX 12 12 ALA A 149 THR A 174 1 26 HELIX 13 13 CYS A 184 VAL A 211 1 28 HELIX 14 14 VAL A 211 ALA A 218 1 8 HELIX 15 15 PRO B 7 ILE B 15 1 9 HELIX 16 16 ARG B 17 TYR B 25 1 9 HELIX 17 17 THR B 36 LYS B 44 1 9 HELIX 18 18 ASP B 47 LEU B 55 1 9 HELIX 19 19 ASP B 66 ALA B 70 5 5 HELIX 20 20 PRO B 71 TYR B 83 1 13 HELIX 21 21 TYR B 83 HIS B 105 1 23 HELIX 22 22 GLY B 114 ILE B 136 1 23 HELIX 23 23 ILE B 136 GLN B 143 1 8 HELIX 24 24 MET B 145 GLN B 148 5 4 HELIX 25 25 ALA B 149 THR B 174 1 26 HELIX 26 26 CYS B 184 VAL B 211 1 28 HELIX 27 27 VAL B 211 ALA B 218 1 8 SSBOND 1 CYS A 184 CYS B 184 1555 1555 2.04 LINK NE2 HIS A 84 ZN ZN A1222 1555 1555 2.15 LINK NE2 HIS A 129 ZN ZN A1221 1555 1555 2.06 LINK OE2 GLU A 133 ZN ZN A1221 1555 1555 1.93 LINK OE1 GLU A 133 ZN ZN A1222 1555 1555 2.16 LINK NE2 HIS A 160 ZN ZN A1221 1555 1555 2.16 LINK NE2 HIS A 204 ZN ZN A1222 1555 1555 2.07 LINK OE1 GLU A 208 ZN ZN A1221 1555 1555 2.21 LINK OE2 GLU A 208 ZN ZN A1222 1555 1555 2.00 LINK ZN ZN A1221 O O A2118 1555 1555 2.01 LINK ZN ZN A1222 O O A2118 1555 1555 1.99 LINK NE2 HIS B 84 ZN ZN B1222 1555 1555 2.18 LINK NE2 HIS B 129 ZN ZN B1221 1555 1555 2.05 LINK OE2 GLU B 133 ZN ZN B1221 1555 1555 1.98 LINK OE1 GLU B 133 ZN ZN B1222 1555 1555 2.16 LINK NE2 HIS B 160 ZN ZN B1221 1555 1555 2.11 LINK NE2 HIS B 204 ZN ZN B1222 1555 1555 2.07 LINK OE1 GLU B 208 ZN ZN B1221 1555 1555 2.19 LINK OE2 GLU B 208 ZN ZN B1222 1555 1555 1.98 LINK ZN ZN B1221 O O B2097 1555 1555 2.04 LINK ZN ZN B1222 O O B2097 1555 1555 1.90 SITE 1 AC1 6 HIS A 129 GLU A 133 HIS A 160 GLU A 208 SITE 2 AC1 6 ZN A1222 O A2118 SITE 1 AC2 6 HIS A 84 GLU A 133 HIS A 204 GLU A 208 SITE 2 AC2 6 ZN A1221 O A2118 SITE 1 AC3 3 HIS A 105 CYS A 184 TRP A 187 SITE 1 AC4 7 HIS A 84 HIS A 129 GLU A 133 HIS A 204 SITE 2 AC4 7 GLU A 208 ZN A1221 ZN A1222 SITE 1 AC5 6 HIS B 129 GLU B 133 HIS B 160 GLU B 208 SITE 2 AC5 6 ZN B1222 O B2097 SITE 1 AC6 6 HIS B 84 GLU B 133 HIS B 204 GLU B 208 SITE 2 AC6 6 ZN B1221 O B2097 SITE 1 AC7 3 HIS B 105 CYS B 184 TRP B 187 SITE 1 AC8 7 HIS B 84 HIS B 129 GLU B 133 HIS B 204 SITE 2 AC8 7 GLU B 208 ZN B1221 ZN B1222 CRYST1 98.454 98.454 126.138 90.00 90.00 90.00 I 41 16 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 0.010157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007928 0.00000