HEADER OXIDOREDUCTASE 06-MAR-25 9QDG TITLE NITRATIDESULFOVIBRIO VULGARIS [FEFE] HYDROGENASE CRYSTALLIZED IN THE TITLE 2 SODIUM PROPIONATE BUFFER AT PH 5.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: FE HYDROGENLYASE SMALL CHAIN; COMPND 5 EC: 1.12.7.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT; COMPND 9 CHAIN: A; COMPND 10 SYNONYM: FE HYDROGENLYASE; COMPND 11 EC: 1.12.7.2; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITRATIDESULFOVIBRIO VULGARIS STR. SOURCE 3 HILDENBOROUGH; SOURCE 4 ORGANISM_TAXID: 882; SOURCE 5 GENE: HYDB, DVU_1770; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: (DELTA)ISCR; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: NITRATIDESULFOVIBRIO VULGARIS STR. SOURCE 11 HILDENBOROUGH; SOURCE 12 ORGANISM_TAXID: 882; SOURCE 13 GENE: HYDA, DVU_1769; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: (DELTA)ISCR KEYWDS [FEFE] HYDROGENASE, IRON-SULFUR CLUSTER, METALLOENZYME, HYDROGEN KEYWDS 2 PRODUCTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BIKBAEV,I.SPAN REVDAT 1 18-MAR-26 9QDG 0 JRNL AUTH K.BIKBAEV,I.SPAN JRNL TITL IMPACT OF THE ACIDIC CONDITIONS ON [FEFE]-HYDROGENASE FROM JRNL TITL 2 NITRATIDESULFOVIBRIO VULGARIS STR. HILDENBOROUGH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 198498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.009 REMARK 3 FREE R VALUE TEST SET COUNT : 9942 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 13766 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 693 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : -0.78100 REMARK 3 B33 (A**2) : 0.54100 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): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9QDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292145978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.688805 REMARK 200 MONOCHROMATOR : SI-111 AND SI-113 REFLECTION REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 198603 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 44.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 32.30 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 4000, 1M LICL, 0.1M REMARK 280 SODIUM PROPIONATE PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.86200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.84200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.85250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.84200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.86200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.85250 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: 8060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 SER A 2 REMARK 465 GLU A 396 REMARK 465 ALA A 397 REMARK 465 TRP A 398 REMARK 465 SER A 399 REMARK 465 HIS A 400 REMARK 465 PRO A 401 REMARK 465 GLN A 402 REMARK 465 PHE A 403 REMARK 465 GLU A 404 REMARK 465 LYS A 405 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 24 NZ REMARK 480 LYS A 93 CD CE NZ REMARK 480 LYS A 96 CE NZ REMARK 480 LYS A 136 NZ REMARK 480 LYS A 247 NZ REMARK 480 THR A 343 CG2 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 HD1 HIS A 351 H GLY A 380 1.22 REMARK 500 HE1 MET A 376 H9 402 A 501 1.23 REMARK 500 H LYS A 346 HD1 HIS A 371 1.24 REMARK 500 HG1 THR A 299 HZ3 LYS A 334 1.27 REMARK 500 HZ2 LYS A 96 O HOH A 601 1.30 REMARK 500 HZ3 LYS A 201 HG SER A 248 1.30 REMARK 500 HG CYS A 35 H HIS A 58 1.34 REMARK 500 HD1 HIS B 91 O HOH B 201 1.50 REMARK 500 HE2 HIS B 91 O HOH B 202 1.54 REMARK 500 O HOH A 743 O HOH A 845 1.90 REMARK 500 NZ LYS A 96 O HOH A 601 2.10 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 H2 VAL B 36 HG1 THR A 343 3655 1.14 REMARK 500 HE1 MET A 54 O HOH A 803 4555 1.22 REMARK 500 CE MET A 54 O HOH A 803 4555 2.09 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 136 CE LYS A 136 NZ -0.254 REMARK 500 GLU A 192 CD GLU A 192 OE1 -0.066 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 146 N - CA - CB ANGL. DEV. = 10.8 DEGREES REMARK 500 LYS A 247 CD - CE - NZ ANGL. DEV. = 19.3 DEGREES REMARK 500 ARG A 308 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 355 NE - CZ - NH1 ANGL. DEV. = -4.6 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 TYR B 75 -59.14 -141.28 REMARK 500 GLU B 77 -50.45 76.64 REMARK 500 PRO B 119 159.44 -46.37 REMARK 500 ARG A 8 -16.50 81.02 REMARK 500 THR A 213 -85.08 -128.29 REMARK 500 LYS A 247 34.04 -146.09 REMARK 500 PHE A 324 79.06 -107.75 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 ARG A 243 0.12 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 504 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 SG REMARK 620 2 SF4 A 504 S1 117.1 REMARK 620 3 SF4 A 504 S2 120.2 105.3 REMARK 620 4 SF4 A 504 S4 101.9 107.3 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 504 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 SF4 A 504 S2 123.5 REMARK 620 3 SF4 A 504 S3 100.7 103.5 REMARK 620 4 SF4 A 504 S4 119.6 102.6 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 504 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 SF4 A 504 S1 119.0 REMARK 620 3 SF4 A 504 S3 112.5 104.7 REMARK 620 4 SF4 A 504 S4 108.4 105.8 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 503 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 503 S2 114.6 REMARK 620 3 SF4 A 503 S3 112.1 103.1 REMARK 620 4 SF4 A 503 S4 117.3 104.1 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 503 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 503 S1 105.0 REMARK 620 3 SF4 A 503 S3 117.0 103.7 REMARK 620 4 SF4 A 503 S4 120.1 104.6 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 503 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 SF4 A 503 S1 118.5 REMARK 620 3 SF4 A 503 S2 100.3 104.8 REMARK 620 4 SF4 A 503 S3 125.3 102.5 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 503 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 SF4 A 503 S1 107.8 REMARK 620 3 SF4 A 503 S2 109.9 105.6 REMARK 620 4 SF4 A 503 S4 125.0 102.6 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 504 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 SF4 A 504 S1 116.5 REMARK 620 3 SF4 A 504 S2 113.7 104.4 REMARK 620 4 SF4 A 504 S3 110.9 104.8 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 502 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 179 SG REMARK 620 2 SF4 A 502 S1 109.1 REMARK 620 3 SF4 A 502 S3 115.3 106.2 REMARK 620 4 SF4 A 502 S4 115.0 105.1 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 502 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 SF4 A 502 S1 107.1 REMARK 620 3 SF4 A 502 S2 104.9 109.3 REMARK 620 4 SF4 A 502 S3 123.7 105.8 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 502 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 378 SG REMARK 620 2 SF4 A 502 S1 108.5 REMARK 620 3 SF4 A 502 S2 116.2 107.5 REMARK 620 4 SF4 A 502 S4 117.1 104.7 101.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 402 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 402 A 501 S1 98.7 REMARK 620 3 402 A 501 S2 97.4 79.6 REMARK 620 4 402 A 501 C3 95.0 166.2 99.4 REMARK 620 5 402 A 501 C4 95.3 83.4 160.2 94.6 REMARK 620 6 402 A 501 C5 176.4 80.8 79.0 85.5 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 502 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 SF4 A 502 S2 118.1 REMARK 620 3 SF4 A 502 S3 105.7 105.5 REMARK 620 4 SF4 A 502 S4 117.9 102.9 105.4 REMARK 620 N 1 2 3 DBREF 9QDG B 36 123 UNP P07603 PHFS_NITV2 36 123 DBREF 9QDG A 1 397 UNP P07598 PHFL_NITV2 1 397 SEQADV 9QDG TRP A 398 UNP P07598 EXPRESSION TAG SEQADV 9QDG SER A 399 UNP P07598 EXPRESSION TAG SEQADV 9QDG HIS A 400 UNP P07598 EXPRESSION TAG SEQADV 9QDG PRO A 401 UNP P07598 EXPRESSION TAG SEQADV 9QDG GLN A 402 UNP P07598 EXPRESSION TAG SEQADV 9QDG PHE A 403 UNP P07598 EXPRESSION TAG SEQADV 9QDG GLU A 404 UNP P07598 EXPRESSION TAG SEQADV 9QDG LYS A 405 UNP P07598 EXPRESSION TAG SEQRES 1 B 88 VAL LYS GLN ILE LYS ASP TYR MET LEU ASP ARG ILE ASN SEQRES 2 B 88 GLY VAL TYR GLY ALA ASP ALA LYS PHE PRO VAL ARG ALA SEQRES 3 B 88 SER GLN ASP ASN THR GLN VAL LYS ALA LEU TYR LYS SER SEQRES 4 B 88 TYR LEU GLU LYS PRO LEU GLY HIS LYS SER HIS ASP LEU SEQRES 5 B 88 LEU HIS THR HIS TRP PHE ASP LYS SER LYS GLY VAL LYS SEQRES 6 B 88 GLU LEU THR THR ALA GLY LYS LEU PRO ASN PRO ARG ALA SEQRES 7 B 88 SER GLU PHE GLU GLY PRO TYR PRO TYR GLU SEQRES 1 A 405 MET SER ARG THR VAL MET GLU ARG ILE GLU TYR GLU MET SEQRES 2 A 405 HIS THR PRO ASP PRO LYS ALA ASP PRO ASP LYS LEU HIS SEQRES 3 A 405 PHE VAL GLN ILE ASP GLU ALA LYS CYS ILE GLY CYS ASP SEQRES 4 A 405 THR CYS SER GLN TYR CYS PRO THR ALA ALA ILE PHE GLY SEQRES 5 A 405 GLU MET GLY GLU PRO HIS SER ILE PRO HIS ILE GLU ALA SEQRES 6 A 405 CYS ILE ASN CYS GLY GLN CYS LEU THR HIS CYS PRO GLU SEQRES 7 A 405 ASN ALA ILE TYR GLU ALA GLN SER TRP VAL PRO GLU VAL SEQRES 8 A 405 GLU LYS LYS LEU LYS ASP GLY LYS VAL LYS CYS ILE ALA SEQRES 9 A 405 MET PRO ALA PRO ALA VAL ARG TYR ALA LEU GLY ASP ALA SEQRES 10 A 405 PHE GLY MET PRO VAL GLY SER VAL THR THR GLY LYS MET SEQRES 11 A 405 LEU ALA ALA LEU GLN LYS LEU GLY PHE ALA HIS CYS TRP SEQRES 12 A 405 ASP THR GLU PHE THR ALA ASP VAL THR ILE TRP GLU GLU SEQRES 13 A 405 GLY SER GLU PHE VAL GLU ARG LEU THR LYS LYS SER ASP SEQRES 14 A 405 MET PRO LEU PRO GLN PHE THR SER CYS CYS PRO GLY TRP SEQRES 15 A 405 GLN LYS TYR ALA GLU THR TYR TYR PRO GLU LEU LEU PRO SEQRES 16 A 405 HIS PHE SER THR CYS LYS SER PRO ILE GLY MET ASN GLY SEQRES 17 A 405 ALA LEU ALA LYS THR TYR GLY ALA GLU ARG MET LYS TYR SEQRES 18 A 405 ASP PRO LYS GLN VAL TYR THR VAL SER ILE MET PRO CYS SEQRES 19 A 405 ILE ALA LYS LYS TYR GLU GLY LEU ARG PRO GLU LEU LYS SEQRES 20 A 405 SER SER GLY MET ARG ASP ILE ASP ALA THR LEU THR THR SEQRES 21 A 405 ARG GLU LEU ALA TYR MET ILE LYS LYS ALA GLY ILE ASP SEQRES 22 A 405 PHE ALA LYS LEU PRO ASP GLY LYS ARG ASP SER LEU MET SEQRES 23 A 405 GLY GLU SER THR GLY GLY ALA THR ILE PHE GLY VAL THR SEQRES 24 A 405 GLY GLY VAL MET GLU ALA ALA LEU ARG PHE ALA TYR GLU SEQRES 25 A 405 ALA VAL THR GLY LYS LYS PRO ASP SER TRP ASP PHE LYS SEQRES 26 A 405 ALA VAL ARG GLY LEU ASP GLY ILE LYS GLU ALA THR VAL SEQRES 27 A 405 ASN VAL GLY GLY THR ASP VAL LYS VAL ALA VAL VAL HIS SEQRES 28 A 405 GLY ALA LYS ARG PHE LYS GLN VAL CYS ASP ASP VAL LYS SEQRES 29 A 405 ALA GLY LYS SER PRO TYR HIS PHE ILE GLU TYR MET ALA SEQRES 30 A 405 CYS PRO GLY GLY CYS VAL CYS GLY GLY GLY GLN PRO VAL SEQRES 31 A 405 MET PRO GLY VAL LEU GLU ALA TRP SER HIS PRO GLN PHE SEQRES 32 A 405 GLU LYS HET 402 A 501 24 HET SF4 A 502 8 HET SF4 A 503 8 HET SF4 A 504 8 HETNAM 402 DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU- HETNAM 2 402 (IMINODIMETHANETHIOLATATO-1KAPPAS:2KAPPAS)-MU- HETNAM 3 402 (OXOMETHYLIDENE)DIIRON(2+) HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 3 402 C7 H5 FE2 N3 O3 S2 2+ FORMUL 4 SF4 3(FE4 S4) FORMUL 7 HOH *421(H2 O) HELIX 1 AA1 GLN B 38 PHE B 57 1 20 HELIX 2 AA2 ALA B 61 ASP B 64 5 4 HELIX 3 AA3 ASN B 65 TYR B 75 1 11 HELIX 4 AA4 GLY B 81 HIS B 89 1 9 HELIX 5 AA5 SER B 96 ALA B 105 1 10 HELIX 6 AA6 ARG B 112 PHE B 116 5 5 HELIX 7 AA7 ASP A 21 LEU A 25 5 5 HELIX 8 AA8 ASP A 39 CYS A 45 1 7 HELIX 9 AA9 HIS A 62 CYS A 66 5 5 HELIX 10 AB1 GLY A 70 CYS A 76 1 7 HELIX 11 AB2 TRP A 87 LYS A 96 1 10 HELIX 12 AB3 PRO A 108 GLY A 119 5 12 HELIX 13 AB4 THR A 126 GLY A 138 1 13 HELIX 14 AB5 ASP A 144 THR A 165 1 22 HELIX 15 AB6 CYS A 179 TYR A 190 1 12 HELIX 16 AB7 PRO A 191 PHE A 197 5 7 HELIX 17 AB8 SER A 202 LYS A 212 1 11 HELIX 18 AB9 THR A 213 LYS A 220 1 8 HELIX 19 AC1 ASP A 222 LYS A 224 5 3 HELIX 20 AC2 ILE A 235 LEU A 242 1 8 HELIX 21 AC3 THR A 260 ALA A 270 1 11 HELIX 22 AC4 ASP A 273 LEU A 277 5 5 HELIX 23 AC5 THR A 290 ILE A 295 1 6 HELIX 24 AC6 PHE A 296 VAL A 298 5 3 HELIX 25 AC7 GLY A 300 GLY A 316 1 17 HELIX 26 AC8 PHE A 324 ARG A 328 5 5 HELIX 27 AC9 ARG A 355 ALA A 365 1 11 HELIX 28 AD1 GLY A 381 GLY A 385 5 5 SHEET 1 AA1 2 THR A 4 MET A 6 0 SHEET 2 AA1 2 ILE A 9 TYR A 11 -1 O ILE A 9 N MET A 6 SHEET 1 AA2 2 VAL A 28 ILE A 30 0 SHEET 2 AA2 2 ILE A 81 GLU A 83 -1 O TYR A 82 N GLN A 29 SHEET 1 AA3 4 HIS A 141 CYS A 142 0 SHEET 2 AA3 4 LYS A 101 PRO A 106 1 N ALA A 104 O HIS A 141 SHEET 3 AA3 4 VAL A 226 MET A 232 1 O VAL A 229 N ILE A 103 SHEET 4 AA3 4 ALA A 256 THR A 259 1 O LEU A 258 N SER A 230 SHEET 1 AA4 4 GLN A 174 PHE A 175 0 SHEET 2 AA4 4 PHE A 372 MET A 376 1 O ILE A 373 N GLN A 174 SHEET 3 AA4 4 THR A 343 HIS A 351 1 N VAL A 350 O GLU A 374 SHEET 4 AA4 4 ILE A 333 VAL A 340 -1 N ALA A 336 O VAL A 347 LINK SG CYS A 35 FE3 SF4 A 504 1555 1555 2.26 LINK SG CYS A 38 FE1 SF4 A 504 1555 1555 2.28 LINK SG CYS A 41 FE2 SF4 A 504 1555 1555 2.23 LINK SG CYS A 45 FE1 SF4 A 503 1555 1555 2.29 LINK SG CYS A 66 FE2 SF4 A 503 1555 1555 2.27 LINK SG CYS A 69 FE4 SF4 A 503 1555 1555 2.30 LINK SG CYS A 72 FE3 SF4 A 503 1555 1555 2.30 LINK SG CYS A 76 FE4 SF4 A 504 1555 1555 2.31 LINK SG CYS A 179 FE2 SF4 A 502 1555 1555 2.28 LINK SG CYS A 234 FE4 SF4 A 502 1555 1555 2.26 LINK SG CYS A 378 FE3 SF4 A 502 1555 1555 2.26 LINK SG CYS A 382 FE1 402 A 501 1555 1555 2.50 LINK SG CYS A 382 FE1 SF4 A 502 1555 1555 2.26 CISPEP 1 LEU B 108 PRO B 109 0 -2.33 CISPEP 2 LEU A 172 PRO A 173 0 1.52 CRYST1 49.724 87.705 89.684 90.00 90.00 90.00 P 21 21 21 4 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 0.020111 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011150 0.00000 CONECT 2058 7657 CONECT 2095 7655 CONECT 2132 7656 CONECT 2192 7647 CONECT 2503 7648 CONECT 2547 7650 CONECT 2582 7649 CONECT 2644 7658 CONECT 4276 7640 CONECT 5159 7642 CONECT 7387 7641 CONECT 7426 7615 7639 CONECT 7615 7426 7617 7618 7624 CONECT 7615 7625 7626 CONECT 7616 7617 7618 7626 7627 CONECT 7616 7628 CONECT 7617 7615 7616 7631 CONECT 7618 7615 7616 7629 CONECT 7619 7624 CONECT 7620 7625 CONECT 7621 7626 CONECT 7622 7627 CONECT 7623 7628 CONECT 7624 7615 7619 CONECT 7625 7615 7620 CONECT 7626 7615 7616 7621 CONECT 7627 7616 7622 CONECT 7628 7616 7623 CONECT 7629 7618 7630 7632 7633 CONECT 7630 7629 7631 7634 CONECT 7631 7617 7630 7635 7636 CONECT 7632 7629 CONECT 7633 7629 CONECT 7634 7630 CONECT 7635 7631 CONECT 7636 7631 CONECT 7639 7426 7644 7645 7646 CONECT 7640 4276 7643 7645 7646 CONECT 7641 7387 7643 7644 7646 CONECT 7642 5159 7643 7644 7645 CONECT 7643 7640 7641 7642 CONECT 7644 7639 7641 7642 CONECT 7645 7639 7640 7642 CONECT 7646 7639 7640 7641 CONECT 7647 2192 7652 7653 7654 CONECT 7648 2503 7651 7653 7654 CONECT 7649 2582 7651 7652 7654 CONECT 7650 2547 7651 7652 7653 CONECT 7651 7648 7649 7650 CONECT 7652 7647 7649 7650 CONECT 7653 7647 7648 7650 CONECT 7654 7647 7648 7649 CONECT 7655 2095 7660 7661 7662 CONECT 7656 2132 7659 7661 7662 CONECT 7657 2058 7659 7660 7662 CONECT 7658 2644 7659 7660 7661 CONECT 7659 7656 7657 7658 CONECT 7660 7655 7657 7658 CONECT 7661 7655 7656 7658 CONECT 7662 7655 7656 7657 MASTER 518 0 4 28 12 0 0 6 4169 2 60 39 END