HEADER OXIDOREDUCTASE 03-NOV-22 8BJ8 TITLE DESULFOVIBRIO DESULFURICANS FEFE HYDROGENASE C178A MUTANT IN HTRANS- TITLE 2 LIKE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FE HYDROGENLYASE; COMPND 5 EC: 1.12.7.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: FE HYDROGENLYASE SMALL CHAIN; COMPND 11 EC: 1.12.7.2; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS; SOURCE 3 ORGANISM_TAXID: 876; SOURCE 4 GENE: HYDA, DVU_1769; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS; SOURCE 9 ORGANISM_TAXID: 876; SOURCE 10 GENE: HYDB, DVU_1770; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS [FEFE] HYDROGENASE, C178A MUTANT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BIKBAEV,I.SPAN REVDAT 4 03-APR-24 8BJ8 1 JRNL REVDAT 3 07-FEB-24 8BJ8 1 REMARK REVDAT 2 04-OCT-23 8BJ8 1 SOURCE REVDAT 1 26-APR-23 8BJ8 0 JRNL AUTH M.A.MARTINI,K.BIKBAEV,Y.PANG,C.LORENT,C.WIEMANN,N.BREUER, JRNL AUTH 2 I.ZEBGER,S.DEBEER,I.SPAN,R.BJORNSSON,J.A.BIRRELL, JRNL AUTH 3 P.RODRIGUEZ-MACIA JRNL TITL BINDING OF EXOGENOUS CYANIDE REVEALS NEW ACTIVE-SITE STATES JRNL TITL 2 IN [FEFE] HYDROGENASES. JRNL REF CHEM SCI V. 14 2826 2023 JRNL REFN ISSN 2041-6520 JRNL PMID 36937599 JRNL DOI 10.1039/D2SC06098A REMARK 2 REMARK 2 RESOLUTION. 1.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0405 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) : 1.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 200362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.893 REMARK 3 FREE R VALUE TEST SET COUNT : 9803 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) : 1.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 13216 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 682 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3684 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 451 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25700 REMARK 3 B22 (A**2) : -0.11500 REMARK 3 B33 (A**2) : -0.14200 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): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.025 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.366 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3806 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3465 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5197 ; 2.089 ; 1.664 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8024 ; 0.693 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 6.358 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 8.030 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;14.327 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.167 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4337 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 795 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 798 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 64 ; 0.232 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1912 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 249 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.099 ; 0.200 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): 1931 ; 0.983 ; 1.060 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1930 ; 0.980 ; 1.060 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2409 ; 1.388 ; 1.909 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2410 ; 1.388 ; 1.909 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1875 ; 1.716 ; 1.189 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1840 ; 1.732 ; 1.194 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2743 ; 2.443 ; 2.126 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2708 ; 2.459 ; 2.129 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 8BJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 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) : 0.8266 REMARK 200 MONOCHROMATOR : NULL 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 : 200463 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 44.602 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 2.14800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 6SG2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LITHIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 30 % POLYETHYLENE GLYCOL 4000, PH 7.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295.15K 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 24.69350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.56250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.70550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.56250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.69350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.70550 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: 8240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 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 GLU A 396 REMARK 465 ALA A 397 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 LYS A 93 CD CE NZ REMARK 470 LYS A 96 CD CE NZ REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS A 166 CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 LYS A 367 CG CD CE NZ 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 19 CE NZ REMARK 480 LYS A 24 NZ REMARK 480 GLU A 53 CD OE1 OE2 REMARK 480 MET A 54 SD REMARK 480 LYS A 99 CD CE NZ REMARK 480 GLN A 135 OE1 REMARK 480 THR A 165 O REMARK 480 LYS A 166 CG REMARK 480 LYS A 167 CG CD CE NZ REMARK 480 ASP A 169 CG OD1 OD2 REMARK 480 LYS A 220 NZ REMARK 480 LYS A 247 NZ REMARK 480 LYS A 269 CE NZ REMARK 480 LYS A 276 CD CE NZ REMARK 480 LYS A 318 CG CD CE NZ REMARK 480 ASP A 320 CB REMARK 480 THR A 343 CG2 REMARK 480 ASP A 344 OD2 REMARK 480 LYS A 367 CA O REMARK 480 GLN B 38 OE1 NE2 REMARK 480 LYS B 40 NZ REMARK 480 LYS B 56 CD CE NZ REMARK 480 LYS B 73 CE NZ REMARK 480 LYS B 97 NZ REMARK 480 GLU B 101 OE1 OE2 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 1.25 REMARK 500 H LYS A 346 HD1 HIS A 371 1.27 REMARK 500 HG CYS A 382 FE1 VHR A 401 1.28 REMARK 500 HH22 ARG A 218 HG SER B 74 1.28 REMARK 500 HZ3 LYS A 201 HG SER A 248 1.28 REMARK 500 HG1 THR A 299 HZ3 LYS A 334 1.31 REMARK 500 HG CYS A 35 H HIS A 58 1.32 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 GLN A 135 CD GLN A 135 OE1 -0.264 REMARK 500 LYS B 40 CE LYS B 40 NZ -0.493 REMARK 500 GLU B 117 CD GLU B 117 OE2 0.067 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 GLN A 135 OE1 - CD - NE2 ANGL. DEV. = -20.5 DEGREES REMARK 500 GLN A 135 CG - CD - OE1 ANGL. DEV. = 22.6 DEGREES REMARK 500 MET A 286 CG - SD - CE ANGL. DEV. = -16.7 DEGREES REMARK 500 ASP A 320 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 355 NH1 - CZ - NH2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 355 NE - CZ - NH1 ANGL. DEV. = -6.4 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 8 -9.68 83.41 REMARK 500 MET A 13 47.19 -85.92 REMARK 500 THR A 213 -85.91 -126.80 REMARK 500 LYS A 247 38.42 -146.55 REMARK 500 TYR B 75 -60.62 -144.18 REMARK 500 GLU B 77 -61.73 79.06 REMARK 500 GLU B 77 -61.27 78.60 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 218 0.08 SIDE CHAIN REMARK 500 ARG A 243 0.11 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 404 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 SG REMARK 620 2 SF4 A 404 S1 102.3 REMARK 620 3 SF4 A 404 S2 120.3 103.9 REMARK 620 4 SF4 A 404 S3 116.0 107.5 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 404 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 SF4 A 404 S1 122.4 REMARK 620 3 SF4 A 404 S2 120.7 102.9 REMARK 620 4 SF4 A 404 S4 97.9 102.9 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 404 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 SF4 A 404 S1 107.2 REMARK 620 3 SF4 A 404 S3 120.0 105.9 REMARK 620 4 SF4 A 404 S4 113.2 105.0 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 403 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 403 S1 117.3 REMARK 620 3 SF4 A 403 S2 112.7 104.2 REMARK 620 4 SF4 A 403 S4 113.8 104.6 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 403 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 403 S1 120.2 REMARK 620 3 SF4 A 403 S3 103.0 104.6 REMARK 620 4 SF4 A 403 S4 117.9 105.3 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 403 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 SF4 A 403 S2 100.1 REMARK 620 3 SF4 A 403 S3 116.7 104.4 REMARK 620 4 SF4 A 403 S4 126.8 102.8 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 403 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 SF4 A 403 S1 124.3 REMARK 620 3 SF4 A 403 S2 110.2 104.2 REMARK 620 4 SF4 A 403 S3 107.7 103.3 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 404 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 SF4 A 404 S2 111.3 REMARK 620 3 SF4 A 404 S3 119.4 103.7 REMARK 620 4 SF4 A 404 S4 109.8 107.4 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 179 SG REMARK 620 2 SF4 A 402 S1 110.2 REMARK 620 3 SF4 A 402 S3 114.8 105.1 REMARK 620 4 SF4 A 402 S4 115.9 105.7 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 SF4 A 402 S1 108.7 REMARK 620 3 SF4 A 402 S2 104.7 109.3 REMARK 620 4 SF4 A 402 S3 123.2 105.4 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 378 SG REMARK 620 2 SF4 A 402 S1 105.9 REMARK 620 3 SF4 A 402 S2 116.4 107.4 REMARK 620 4 SF4 A 402 S4 118.2 105.4 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 VHR A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 VHR A 401 S2 97.1 REMARK 620 3 VHR A 401 C3 87.2 92.6 REMARK 620 4 VHR A 401 S1 93.4 85.4 178.0 REMARK 620 5 VHR A 401 C4 91.9 168.4 95.1 86.8 REMARK 620 6 VHR A 401 C5 172.9 88.1 87.8 91.7 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 SF4 A 402 S2 117.3 REMARK 620 3 SF4 A 402 S3 105.4 105.3 REMARK 620 4 SF4 A 402 S4 119.7 103.2 104.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6SG2 RELATED DB: PDB REMARK 900 WILDTYPE IN HINACT STATE REMARK 900 RELATED ID: 1HFE RELATED DB: PDB REMARK 900 WILDTYPE IN HOX/HRED STATE DBREF 8BJ8 A 2 397 UNP P07598 PHFL_DESVH 2 397 DBREF 8BJ8 B 36 123 UNP P07603 PHFS_DESVH 36 123 SEQADV 8BJ8 ALA A 178 UNP P07598 CYS 178 ENGINEERED MUTATION SEQRES 1 A 396 SER ARG THR VAL MET GLU ARG ILE GLU TYR GLU MET HIS SEQRES 2 A 396 THR PRO ASP PRO LYS ALA ASP PRO ASP LYS LEU HIS PHE SEQRES 3 A 396 VAL GLN ILE ASP GLU ALA LYS CYS ILE GLY CYS ASP THR SEQRES 4 A 396 CYS SER GLN TYR CYS PRO THR ALA ALA ILE PHE GLY GLU SEQRES 5 A 396 MET GLY GLU PRO HIS SER ILE PRO HIS ILE GLU ALA CYS SEQRES 6 A 396 ILE ASN CYS GLY GLN CYS LEU THR HIS CYS PRO GLU ASN SEQRES 7 A 396 ALA ILE TYR GLU ALA GLN SER TRP VAL PRO GLU VAL GLU SEQRES 8 A 396 LYS LYS LEU LYS ASP GLY LYS VAL LYS CYS ILE ALA MET SEQRES 9 A 396 PRO ALA PRO ALA VAL ARG TYR ALA LEU GLY ASP ALA PHE SEQRES 10 A 396 GLY MET PRO VAL GLY SER VAL THR THR GLY LYS MET LEU SEQRES 11 A 396 ALA ALA LEU GLN LYS LEU GLY PHE ALA HIS CYS TRP ASP SEQRES 12 A 396 THR GLU PHE THR ALA ASP VAL THR ILE TRP GLU GLU GLY SEQRES 13 A 396 SER GLU PHE VAL GLU ARG LEU THR LYS LYS SER ASP MET SEQRES 14 A 396 PRO LEU PRO GLN PHE THR SER ALA CYS PRO GLY TRP GLN SEQRES 15 A 396 LYS TYR ALA GLU THR TYR TYR PRO GLU LEU LEU PRO HIS SEQRES 16 A 396 PHE SER THR CYS LYS SER PRO ILE GLY MET ASN GLY ALA SEQRES 17 A 396 LEU ALA LYS THR TYR GLY ALA GLU ARG MET LYS TYR ASP SEQRES 18 A 396 PRO LYS GLN VAL TYR THR VAL SER ILE MET PRO CYS ILE SEQRES 19 A 396 ALA LYS LYS TYR GLU GLY LEU ARG PRO GLU LEU LYS SER SEQRES 20 A 396 SER GLY MET ARG ASP ILE ASP ALA THR LEU THR THR ARG SEQRES 21 A 396 GLU LEU ALA TYR MET ILE LYS LYS ALA GLY ILE ASP PHE SEQRES 22 A 396 ALA LYS LEU PRO ASP GLY LYS ARG ASP SER LEU MET GLY SEQRES 23 A 396 GLU SER THR GLY GLY ALA THR ILE PHE GLY VAL THR GLY SEQRES 24 A 396 GLY VAL MET GLU ALA ALA LEU ARG PHE ALA TYR GLU ALA SEQRES 25 A 396 VAL THR GLY LYS LYS PRO ASP SER TRP ASP PHE LYS ALA SEQRES 26 A 396 VAL ARG GLY LEU ASP GLY ILE LYS GLU ALA THR VAL ASN SEQRES 27 A 396 VAL GLY GLY THR ASP VAL LYS VAL ALA VAL VAL HIS GLY SEQRES 28 A 396 ALA LYS ARG PHE LYS GLN VAL CYS ASP ASP VAL LYS ALA SEQRES 29 A 396 GLY LYS SER PRO TYR HIS PHE ILE GLU TYR MET ALA CYS SEQRES 30 A 396 PRO GLY GLY CYS VAL CYS GLY GLY GLY GLN PRO VAL MET SEQRES 31 A 396 PRO GLY VAL LEU GLU ALA 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 HET VHR A 401 26 HET SF4 A 402 8 HET SF4 A 403 8 HET SF4 A 404 8 HETNAM VHR BINUCLEAR [FEFE], DI(THIOMETHYL)AMINE, CARBON MONOXIDE, HETNAM 2 VHR CYANIDE CLUSTER (-CN FORM) HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 3 VHR C8 H5 FE2 N4 O3 S2 1- FORMUL 4 SF4 3(FE4 S4) FORMUL 7 HOH *451(H2 O) HELIX 1 AA1 ASP A 21 LEU A 25 5 5 HELIX 2 AA2 ASP A 39 CYS A 45 1 7 HELIX 3 AA3 HIS A 62 CYS A 66 5 5 HELIX 4 AA4 GLY A 70 CYS A 76 1 7 HELIX 5 AA5 TRP A 87 LYS A 96 1 10 HELIX 6 AA6 PRO A 108 GLY A 119 5 12 HELIX 7 AA7 THR A 126 GLY A 138 1 13 HELIX 8 AA8 ASP A 144 THR A 165 1 22 HELIX 9 AA9 CYS A 179 TYR A 190 1 12 HELIX 10 AB1 PRO A 191 PHE A 197 5 7 HELIX 11 AB2 SER A 202 LYS A 212 1 11 HELIX 12 AB3 THR A 213 LYS A 220 1 8 HELIX 13 AB4 ASP A 222 LYS A 224 5 3 HELIX 14 AB5 ILE A 235 LEU A 242 1 8 HELIX 15 AB6 THR A 260 ALA A 270 1 11 HELIX 16 AB7 ASP A 273 LEU A 277 5 5 HELIX 17 AB8 THR A 290 ILE A 295 1 6 HELIX 18 AB9 PHE A 296 VAL A 298 5 3 HELIX 19 AC1 GLY A 300 GLY A 316 1 17 HELIX 20 AC2 PHE A 324 ARG A 328 5 5 HELIX 21 AC3 ARG A 355 GLY A 366 1 12 HELIX 22 AC4 GLY A 381 GLY A 385 5 5 HELIX 23 AC5 GLN B 38 LYS B 56 1 19 HELIX 24 AC6 ALA B 61 ASP B 64 5 4 HELIX 25 AC7 ASN B 65 TYR B 75 1 11 HELIX 26 AC8 GLY B 81 HIS B 89 1 9 HELIX 27 AC9 SER B 96 ALA B 105 1 10 HELIX 28 AD1 ARG B 112 GLU B 117 5 6 SHEET 1 AA1 2 ARG A 3 MET A 6 0 SHEET 2 AA1 2 ILE A 9 GLU A 12 -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 TYR A 227 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 VAL A 338 O VAL A 345 LINK SG CYS A 35 FE4 SF4 A 404 1555 1555 2.28 LINK SG CYS A 38 FE3 SF4 A 404 1555 1555 2.28 LINK SG CYS A 41 FE2 SF4 A 404 1555 1555 2.26 LINK SG CYS A 45 FE3 SF4 A 403 1555 1555 2.31 LINK SG CYS A 66 FE2 SF4 A 403 1555 1555 2.29 LINK SG CYS A 69 FE1 SF4 A 403 1555 1555 2.30 LINK SG CYS A 72 FE4 SF4 A 403 1555 1555 2.29 LINK SG CYS A 76 FE1 SF4 A 404 1555 1555 2.29 LINK SG CYS A 179 FE2 SF4 A 402 1555 1555 2.27 LINK SG CYS A 234 FE4 SF4 A 402 1555 1555 2.27 LINK SG CYS A 378 FE3 SF4 A 402 1555 1555 2.27 LINK SG CYS A 382 FE1 VHR A 401 1555 1555 2.42 LINK SG CYS A 382 FE1 SF4 A 402 1555 1555 2.28 CISPEP 1 LEU A 172 PRO A 173 0 -8.60 CISPEP 2 LEU B 108 PRO B 109 0 3.81 CRYST1 49.387 87.411 89.125 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 0.020248 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011220 0.00000