HEADER OXIDOREDUCTASE 19-NOV-18 6N4K TITLE DITHIONITE-REDUCED NUCLEOTIDE-FREE FORM OF THE NITROGENASE FE-PROTEIN TITLE 2 FROM A. VINELANDII COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGENASE IRON PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NITROGENASE FE PROTEIN 1,NITROGENASE COMPONENT II, COMPND 5 NITROGENASE REDUCTASE; COMPND 6 EC: 1.18.6.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354 KEYWDS NITROGENASE, IRON SULFUR CLUSTER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.B.WENKE,T.SPATZAL,D.C.REES REVDAT 4 11-OCT-23 6N4K 1 REMARK LINK REVDAT 3 01-JAN-20 6N4K 1 REMARK REVDAT 2 27-MAR-19 6N4K 1 JRNL REVDAT 1 13-FEB-19 6N4K 0 JRNL AUTH B.B.WENKE,T.SPATZAL,D.C.REES JRNL TITL SITE-SPECIFIC OXIDATION STATE ASSIGNMENTS OF THE IRON ATOMS JRNL TITL 2 IN THE [4FE:4S]2+/1+/0STATES OF THE NITROGENASE FE-PROTEIN. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 58 3894 2019 JRNL REFN ESSN 1521-3773 JRNL PMID 30698901 JRNL DOI 10.1002/ANIE.201813966 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 46085 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2369 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2307 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.1900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4093 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.84000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.208 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.903 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4120 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3912 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5565 ; 1.703 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9067 ; 1.597 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 538 ; 6.442 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;32.720 ;23.467 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;14.427 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 554 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4652 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 784 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 8031 ; 1.283 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 36 ;21.645 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7990 ;12.071 ; 5.000 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 1 A 271 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1734 -11.8226 36.5903 REMARK 3 T TENSOR REMARK 3 T11: 0.0276 T22: 0.0100 REMARK 3 T33: 0.1015 T12: 0.0032 REMARK 3 T13: -0.0074 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 1.8500 L22: 1.8368 REMARK 3 L33: 2.2868 L12: -0.4678 REMARK 3 L13: -0.3161 L23: -0.0662 REMARK 3 S TENSOR REMARK 3 S11: 0.0577 S12: 0.1058 S13: -0.0836 REMARK 3 S21: 0.1713 S22: -0.0195 S23: 0.0313 REMARK 3 S31: 0.0754 S32: -0.0014 S33: -0.0382 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 1 B 271 REMARK 3 ORIGIN FOR THE GROUP (A): -40.1541 -8.6424 17.6813 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.1284 REMARK 3 T33: 0.0481 T12: 0.0111 REMARK 3 T13: -0.0052 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 3.6121 L22: 2.9091 REMARK 3 L33: 1.8339 L12: 1.0423 REMARK 3 L13: -0.5544 L23: 0.2994 REMARK 3 S TENSOR REMARK 3 S11: -0.1014 S12: 0.3588 S13: -0.0864 REMARK 3 S21: -0.3245 S22: 0.0480 S23: 0.0262 REMARK 3 S31: 0.0107 S32: -0.0240 S33: 0.0534 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 6N4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.756 REMARK 200 RESOLUTION RANGE LOW (A) : 108.055 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 REMARK 200 R SYM FOR SHELL (I) : 0.20800 REMARK 200 FOR SHELL : 3.600 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: 1G5P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OF 40% PEG 1000, 0.2 M NACL, 0.1 M REMARK 280 MES/OH PH 6.5, 10% 2,2,2-TRIFLUOROETHANOL, 5 MM DITHIONITE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.81000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.59950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.81000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.59950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 272 REMARK 465 ILE A 273 REMARK 465 MET A 274 REMARK 465 GLU A 275 REMARK 465 VAL A 276 REMARK 465 GLU A 277 REMARK 465 ASP A 278 REMARK 465 GLU A 279 REMARK 465 SER A 280 REMARK 465 ILE A 281 REMARK 465 VAL A 282 REMARK 465 GLY A 283 REMARK 465 LYS A 284 REMARK 465 THR A 285 REMARK 465 ALA A 286 REMARK 465 GLU A 287 REMARK 465 GLU A 288 REMARK 465 VAL A 289 REMARK 465 GLY B 272 REMARK 465 ILE B 273 REMARK 465 MET B 274 REMARK 465 GLU B 275 REMARK 465 VAL B 276 REMARK 465 GLU B 277 REMARK 465 ASP B 278 REMARK 465 GLU B 279 REMARK 465 SER B 280 REMARK 465 ILE B 281 REMARK 465 VAL B 282 REMARK 465 GLY B 283 REMARK 465 LYS B 284 REMARK 465 THR B 285 REMARK 465 ALA B 286 REMARK 465 GLU B 287 REMARK 465 GLU B 288 REMARK 465 VAL B 289 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 ALA A 1 N CA CB REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 ALA B 1 N CA CB REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 32 CD CE NZ REMARK 480 LYS A 52 CD CE NZ REMARK 480 GLU A 63 CD OE1 OE2 REMARK 480 LYS A 233 CD CE NZ REMARK 480 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 32 CD CE NZ REMARK 480 LYS B 52 CD CE NZ REMARK 480 LYS B 233 CD CE NZ REMARK 480 ARG B 245 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 CE MET B 29 NH1 ARG B 245 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS B 52 OE2 GLU B 73 4445 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 52 CG LYS A 52 CD -0.273 REMARK 500 GLU A 63 CG GLU A 63 CD -0.227 REMARK 500 LYS B 32 CG LYS B 32 CD 0.269 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 MET A 2 132.14 176.97 REMARK 500 ASP A 118 46.19 -68.39 REMARK 500 THR A 205 -156.82 -121.94 REMARK 500 ALA B 53 99.45 -172.26 REMARK 500 ASP B 117 54.96 -103.65 REMARK 500 SER B 174 51.98 -155.71 REMARK 500 THR B 205 -156.76 -120.43 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 GLY B 175 SER B 176 -147.01 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 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 SF4 A 301 S2 115.6 REMARK 620 3 SF4 A 301 S3 114.7 103.2 REMARK 620 4 SF4 A 301 S4 112.2 104.0 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 132 SG REMARK 620 2 SF4 A 301 S1 119.7 REMARK 620 3 SF4 A 301 S3 111.7 104.7 REMARK 620 4 SF4 A 301 S4 110.8 102.3 106.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 97 SG REMARK 620 2 SF4 A 301 S1 116.6 REMARK 620 3 SF4 A 301 S2 110.6 106.7 REMARK 620 4 SF4 A 301 S4 116.1 101.5 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 132 SG REMARK 620 2 SF4 A 301 S1 110.9 REMARK 620 3 SF4 A 301 S2 111.3 106.2 REMARK 620 4 SF4 A 301 S3 119.2 105.3 102.9 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 301 DBREF 6N4K A 1 289 UNP P00459 NIFH1_AZOVI 2 290 DBREF 6N4K B 1 289 UNP P00459 NIFH1_AZOVI 2 290 SEQRES 1 A 289 ALA MET ARG GLN CYS ALA ILE TYR GLY LYS GLY GLY ILE SEQRES 2 A 289 GLY LYS SER THR THR THR GLN ASN LEU VAL ALA ALA LEU SEQRES 3 A 289 ALA GLU MET GLY LYS LYS VAL MET ILE VAL GLY CYS ASP SEQRES 4 A 289 PRO LYS ALA ASP SER THR ARG LEU ILE LEU HIS SER LYS SEQRES 5 A 289 ALA GLN ASN THR ILE MET GLU MET ALA ALA GLU ALA GLY SEQRES 6 A 289 THR VAL GLU ASP LEU GLU LEU GLU ASP VAL LEU LYS ALA SEQRES 7 A 289 GLY TYR GLY GLY VAL LYS CYS VAL GLU SER GLY GLY PRO SEQRES 8 A 289 GLU PRO GLY VAL GLY CYS ALA GLY ARG GLY VAL ILE THR SEQRES 9 A 289 ALA ILE ASN PHE LEU GLU GLU GLU GLY ALA TYR GLU ASP SEQRES 10 A 289 ASP LEU ASP PHE VAL PHE TYR ASP VAL LEU GLY ASP VAL SEQRES 11 A 289 VAL CYS GLY GLY PHE ALA MET PRO ILE ARG GLU ASN LYS SEQRES 12 A 289 ALA GLN GLU ILE TYR ILE VAL CYS SER GLY GLU MET MET SEQRES 13 A 289 ALA MET TYR ALA ALA ASN ASN ILE SER LYS GLY ILE VAL SEQRES 14 A 289 LYS TYR ALA ASN SER GLY SER VAL ARG LEU GLY GLY LEU SEQRES 15 A 289 ILE CYS ASN SER ARG ASN THR ASP ARG GLU ASP GLU LEU SEQRES 16 A 289 ILE ILE ALA LEU ALA ASN LYS LEU GLY THR GLN MET ILE SEQRES 17 A 289 HIS PHE VAL PRO ARG ASP ASN VAL VAL GLN ARG ALA GLU SEQRES 18 A 289 ILE ARG ARG MET THR VAL ILE GLU TYR ASP PRO LYS ALA SEQRES 19 A 289 LYS GLN ALA ASP GLU TYR ARG ALA LEU ALA ARG LYS VAL SEQRES 20 A 289 VAL ASP ASN LYS LEU LEU VAL ILE PRO ASN PRO ILE THR SEQRES 21 A 289 MET ASP GLU LEU GLU GLU LEU LEU MET GLU PHE GLY ILE SEQRES 22 A 289 MET GLU VAL GLU ASP GLU SER ILE VAL GLY LYS THR ALA SEQRES 23 A 289 GLU GLU VAL SEQRES 1 B 289 ALA MET ARG GLN CYS ALA ILE TYR GLY LYS GLY GLY ILE SEQRES 2 B 289 GLY LYS SER THR THR THR GLN ASN LEU VAL ALA ALA LEU SEQRES 3 B 289 ALA GLU MET GLY LYS LYS VAL MET ILE VAL GLY CYS ASP SEQRES 4 B 289 PRO LYS ALA ASP SER THR ARG LEU ILE LEU HIS SER LYS SEQRES 5 B 289 ALA GLN ASN THR ILE MET GLU MET ALA ALA GLU ALA GLY SEQRES 6 B 289 THR VAL GLU ASP LEU GLU LEU GLU ASP VAL LEU LYS ALA SEQRES 7 B 289 GLY TYR GLY GLY VAL LYS CYS VAL GLU SER GLY GLY PRO SEQRES 8 B 289 GLU PRO GLY VAL GLY CYS ALA GLY ARG GLY VAL ILE THR SEQRES 9 B 289 ALA ILE ASN PHE LEU GLU GLU GLU GLY ALA TYR GLU ASP SEQRES 10 B 289 ASP LEU ASP PHE VAL PHE TYR ASP VAL LEU GLY ASP VAL SEQRES 11 B 289 VAL CYS GLY GLY PHE ALA MET PRO ILE ARG GLU ASN LYS SEQRES 12 B 289 ALA GLN GLU ILE TYR ILE VAL CYS SER GLY GLU MET MET SEQRES 13 B 289 ALA MET TYR ALA ALA ASN ASN ILE SER LYS GLY ILE VAL SEQRES 14 B 289 LYS TYR ALA ASN SER GLY SER VAL ARG LEU GLY GLY LEU SEQRES 15 B 289 ILE CYS ASN SER ARG ASN THR ASP ARG GLU ASP GLU LEU SEQRES 16 B 289 ILE ILE ALA LEU ALA ASN LYS LEU GLY THR GLN MET ILE SEQRES 17 B 289 HIS PHE VAL PRO ARG ASP ASN VAL VAL GLN ARG ALA GLU SEQRES 18 B 289 ILE ARG ARG MET THR VAL ILE GLU TYR ASP PRO LYS ALA SEQRES 19 B 289 LYS GLN ALA ASP GLU TYR ARG ALA LEU ALA ARG LYS VAL SEQRES 20 B 289 VAL ASP ASN LYS LEU LEU VAL ILE PRO ASN PRO ILE THR SEQRES 21 B 289 MET ASP GLU LEU GLU GLU LEU LEU MET GLU PHE GLY ILE SEQRES 22 B 289 MET GLU VAL GLU ASP GLU SER ILE VAL GLY LYS THR ALA SEQRES 23 B 289 GLU GLU VAL HET SF4 A 301 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 3 SF4 FE4 S4 FORMUL 4 HOH *46(H2 O) HELIX 1 AA1 GLY A 14 MET A 29 1 16 HELIX 2 AA2 THR A 45 HIS A 50 1 6 HELIX 3 AA3 THR A 56 GLY A 65 1 10 HELIX 4 AA4 THR A 66 LEU A 70 5 5 HELIX 5 AA5 GLU A 71 LEU A 76 1 6 HELIX 6 AA6 TYR A 80 GLY A 82 5 3 HELIX 7 AA7 CYS A 97 GLU A 112 1 16 HELIX 8 AA8 ALA A 136 GLU A 141 1 6 HELIX 9 AA9 GLU A 154 ALA A 172 1 19 HELIX 10 AB1 ARG A 191 GLY A 204 1 14 HELIX 11 AB2 ASP A 214 ARG A 223 1 10 HELIX 12 AB3 THR A 226 ASP A 231 1 6 HELIX 13 AB4 ALA A 234 ASN A 250 1 17 HELIX 14 AB5 THR A 260 PHE A 271 1 12 HELIX 15 AB6 GLY B 14 MET B 29 1 16 HELIX 16 AB7 THR B 45 HIS B 50 1 6 HELIX 17 AB8 THR B 56 GLY B 65 1 10 HELIX 18 AB9 GLU B 71 LEU B 76 1 6 HELIX 19 AC1 TYR B 80 GLY B 82 5 3 HELIX 20 AC2 CYS B 97 GLY B 113 1 17 HELIX 21 AC3 ALA B 114 ASP B 117 5 4 HELIX 22 AC4 ALA B 136 GLU B 141 1 6 HELIX 23 AC5 GLU B 154 ASN B 173 1 20 HELIX 24 AC6 ARG B 191 GLY B 204 1 14 HELIX 25 AC7 ASP B 214 ARG B 223 1 10 HELIX 26 AC8 THR B 226 ASP B 231 1 6 HELIX 27 AC9 ALA B 234 ASP B 249 1 16 HELIX 28 AD1 THR B 260 PHE B 271 1 12 SHEET 1 AA1 8 LYS A 77 ALA A 78 0 SHEET 2 AA1 8 LYS A 84 GLU A 87 -1 O CYS A 85 N LYS A 77 SHEET 3 AA1 8 VAL A 33 CYS A 38 1 N GLY A 37 O VAL A 86 SHEET 4 AA1 8 PHE A 121 LEU A 127 1 O ASP A 125 N CYS A 38 SHEET 5 AA1 8 ARG A 3 GLY A 9 1 N CYS A 5 O VAL A 122 SHEET 6 AA1 8 GLU A 146 CYS A 151 1 O TYR A 148 N ALA A 6 SHEET 7 AA1 8 ARG A 178 ASN A 185 1 O GLY A 180 N ILE A 147 SHEET 8 AA1 8 MET A 207 VAL A 211 1 O VAL A 211 N CYS A 184 SHEET 1 AA2 8 LYS B 77 ALA B 78 0 SHEET 2 AA2 8 LYS B 84 GLU B 87 -1 O CYS B 85 N LYS B 77 SHEET 3 AA2 8 VAL B 33 CYS B 38 1 N GLY B 37 O VAL B 86 SHEET 4 AA2 8 PHE B 121 LEU B 127 1 O ASP B 125 N CYS B 38 SHEET 5 AA2 8 ARG B 3 GLY B 9 1 N ILE B 7 O VAL B 126 SHEET 6 AA2 8 GLU B 146 CYS B 151 1 O VAL B 150 N TYR B 8 SHEET 7 AA2 8 ARG B 178 ASN B 185 1 O GLY B 180 N ILE B 147 SHEET 8 AA2 8 MET B 207 VAL B 211 1 O VAL B 211 N CYS B 184 LINK SG CYS A 97 FE1 SF4 A 301 1555 1555 2.36 LINK SG CYS A 132 FE2 SF4 A 301 1555 1555 2.30 LINK FE3 SF4 A 301 SG CYS B 97 1555 1555 2.35 LINK FE4 SF4 A 301 SG CYS B 132 1555 1555 2.35 SITE 1 AC1 8 CYS A 97 ALA A 98 CYS A 132 GLY A 134 SITE 2 AC1 8 CYS B 97 ALA B 98 CYS B 132 GLY B 134 CRYST1 103.620 45.199 108.772 90.00 96.58 90.00 C 1 2 1 8 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 0.009651 0.000000 0.001114 0.00000 SCALE2 0.000000 0.022124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009255 0.00000