HEADER OXIDOREDUCTASE 08-FEB-24 8RYH TITLE NITRATIDESULFOVIBRIO VULGARIS [FEFE]-HYDROGENASE [FEFE]-HYDROGENASE TITLE 2 VARIANT WITH BOTH SUBUNITS LINKED BY A LINKER PEPTIDE DERIVED FROM A TITLE 3 GROUP A1 TYPE [FEFE]-HYDROGENASE OF VEILLONELLA ATYPICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT,PERIPLASMIC [FE] COMPND 3 HYDROGENASE SMALL SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: FE HYDROGENLYASE,FE HYDROGENLYASE SMALL CHAIN; COMPND 6 EC: 1.12.7.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITRATIDESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881; SOURCE 4 GENE: HYDA, DVU_1769, HYDB, DVU_1770; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: (DELTA)ISCR KEYWDS [FEFE] HYDROGENASE, IRON-SULFUR CLUSTER, METALLOENZYME, HYDROGEN KEYWDS 2 PRODUCTION, FUSION PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BIKBAEV,J.JAENECKE,M.WINKLER,I.SPAN REVDAT 2 25-FEB-26 8RYH 1 TITLE SOURCE JRNL REVDAT 1 19-FEB-25 8RYH 0 JRNL AUTH M.H.WINKLER,J.JAENECKE,K.BIKBAEV,J.BRONOLD,S.YADAV, JRNL AUTH 2 U.P.APFEL,J.A.BIRRELL,I.SPAN,N.PLUMERE,C.LEGER,M.MALAGNINI JRNL TITL SUBUNIT FUSION UNLOCKS RAPID IN VITRO MATURATION FOR SLOWLY JRNL TITL 2 ACTIVATING HETERODIMERIC [FEFE]-HYDROGENASES JRNL REF CHEM SCI 2026 JRNL REFN ESSN 2041-6539 JRNL DOI 10.1039/D5SC07299A REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 41647 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) : 0.205 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.006 REMARK 3 FREE R VALUE TEST SET COUNT : 2085 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2008 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3602 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90300 REMARK 3 B22 (A**2) : -1.05400 REMARK 3 B33 (A**2) : 0.47300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71900 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.102 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3770 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3481 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5136 ; 1.861 ; 1.848 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8095 ; 0.569 ; 1.772 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ; 9.625 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 633 ;13.080 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 549 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4319 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 789 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 831 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 45 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1839 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 168 ; 0.136 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.116 ; 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): 1880 ; 1.601 ; 1.943 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1880 ; 1.600 ; 1.943 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2348 ; 2.364 ; 3.485 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2349 ; 2.365 ; 3.486 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1890 ; 1.920 ; 2.124 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1891 ; 1.920 ; 2.123 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2744 ; 2.981 ; 3.814 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2745 ; 2.980 ; 3.814 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 8RYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-23 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) : 1.033 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 : 41648 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 45.402 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 45.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.05400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 26.40 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 (%): 40.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LITHIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 25 % POLYETHYLENE GLYCOL 4000, PH 7.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 53.05900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.30150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.05900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.30150 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: 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 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 LYS A 392 REMARK 465 LEU A 393 REMARK 465 PRO A 394 REMARK 465 MET A 395 REMARK 465 ALA A 396 REMARK 465 ASP A 397 REMARK 465 LYS A 398 REMARK 465 TYR A 479 REMARK 465 GLU A 480 REMARK 465 SER A 481 REMARK 465 ALA A 482 REMARK 465 TRP A 483 REMARK 465 SER A 484 REMARK 465 HIS A 485 REMARK 465 PRO A 486 REMARK 465 GLN A 487 REMARK 465 PHE A 488 REMARK 465 GLU A 489 REMARK 465 LYS A 490 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 430 CG CD CE NZ 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 HG2 ARG A 111 HG1 THR A 127 1.09 REMARK 500 HD1 HIS A 351 H GLY A 380 1.16 REMARK 500 H LYS A 346 HD2 HIS A 371 1.26 REMARK 500 HG CYS A 382 FE1 402 A 504 1.27 REMARK 500 HG CYS A 35 H HIS A 58 1.27 REMARK 500 OD2 ASP A 116 HH21 ARG A 403 1.58 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 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 111 CB - CA - C ANGL. DEV. = -14.3 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 -24.30 77.36 REMARK 500 ASP A 39 8.83 81.13 REMARK 500 THR A 213 -82.33 -120.25 REMARK 500 PRO A 233 25.90 -78.15 REMARK 500 LYS A 247 37.73 -148.29 REMARK 500 MET A 286 51.65 -140.43 REMARK 500 SER A 368 128.67 -39.47 REMARK 500 LEU A 433 -53.92 70.23 REMARK 500 GLU A 434 -57.43 81.68 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 0.09 SIDE CHAIN REMARK 500 ARG A 417 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 502 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 SG REMARK 620 2 SF4 A 502 S2 118.3 REMARK 620 3 SF4 A 502 S3 118.8 106.0 REMARK 620 4 SF4 A 502 S4 102.4 105.5 103.9 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 38 SG REMARK 620 2 SF4 A 502 S1 101.4 REMARK 620 3 SF4 A 502 S3 117.4 106.6 REMARK 620 4 SF4 A 502 S4 122.1 103.2 104.3 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 41 SG REMARK 620 2 SF4 A 502 S1 114.5 REMARK 620 3 SF4 A 502 S2 118.1 104.8 REMARK 620 4 SF4 A 502 S4 107.8 104.6 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 501 S1 112.9 REMARK 620 3 SF4 A 501 S3 114.2 102.1 REMARK 620 4 SF4 A 501 S4 115.6 105.6 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 501 S1 117.3 REMARK 620 3 SF4 A 501 S2 104.2 103.8 REMARK 620 4 SF4 A 501 S4 119.2 105.0 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 SF4 A 501 S1 121.8 REMARK 620 3 SF4 A 501 S2 117.8 103.9 REMARK 620 4 SF4 A 501 S3 103.2 104.4 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 SF4 A 501 S2 109.5 REMARK 620 3 SF4 A 501 S3 110.3 104.7 REMARK 620 4 SF4 A 501 S4 122.5 104.7 103.7 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 76 SG REMARK 620 2 SF4 A 502 S1 109.9 REMARK 620 3 SF4 A 502 S2 118.3 105.4 REMARK 620 4 SF4 A 502 S3 111.7 105.6 105.0 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 179 SG REMARK 620 2 SF4 A 503 S1 119.3 REMARK 620 3 SF4 A 503 S2 114.0 102.0 REMARK 620 4 SF4 A 503 S4 111.0 105.5 103.3 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 234 SG REMARK 620 2 SF4 A 503 S2 124.3 REMARK 620 3 SF4 A 503 S3 104.3 103.9 REMARK 620 4 SF4 A 503 S4 108.9 105.2 109.7 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 378 SG REMARK 620 2 SF4 A 503 S1 118.5 REMARK 620 3 SF4 A 503 S3 117.9 103.1 REMARK 620 4 SF4 A 503 S4 105.6 103.3 107.2 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 382 SG REMARK 620 2 SF4 A 503 S1 122.8 REMARK 620 3 SF4 A 503 S2 104.9 102.5 REMARK 620 4 SF4 A 503 S3 117.1 103.2 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 402 A 504 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 402 A 504 S1 95.7 REMARK 620 3 402 A 504 S2 97.5 81.1 REMARK 620 4 402 A 504 C3 90.9 172.1 93.8 REMARK 620 5 402 A 504 C4 91.8 88.8 166.9 95.3 REMARK 620 6 402 A 504 C5 177.1 82.9 84.8 90.7 85.6 REMARK 620 N 1 2 3 4 5 DBREF 8RYH A 1 389 UNP P07598 PHFL_DESVH 1 389 DBREF 8RYH A 403 480 UNP P07603 PHFS_DESVH 46 123 SEQADV 8RYH ARG A 390 UNP P07598 LINKER SEQADV 8RYH VAL A 391 UNP P07598 LINKER SEQADV 8RYH LYS A 392 UNP P07598 LINKER SEQADV 8RYH LEU A 393 UNP P07598 LINKER SEQADV 8RYH PRO A 394 UNP P07598 LINKER SEQADV 8RYH MET A 395 UNP P07598 LINKER SEQADV 8RYH ALA A 396 UNP P07598 LINKER SEQADV 8RYH ASP A 397 UNP P07598 LINKER SEQADV 8RYH LYS A 398 UNP P07598 LINKER SEQADV 8RYH ALA A 399 UNP P07598 LINKER SEQADV 8RYH ARG A 400 UNP P07598 LINKER SEQADV 8RYH GLU A 401 UNP P07598 LINKER SEQADV 8RYH ALA A 402 UNP P07598 LINKER SEQADV 8RYH SER A 481 UNP P07603 EXPRESSION TAG SEQADV 8RYH ALA A 482 UNP P07603 EXPRESSION TAG SEQADV 8RYH TRP A 483 UNP P07603 EXPRESSION TAG SEQADV 8RYH SER A 484 UNP P07603 EXPRESSION TAG SEQADV 8RYH HIS A 485 UNP P07603 EXPRESSION TAG SEQADV 8RYH PRO A 486 UNP P07603 EXPRESSION TAG SEQADV 8RYH GLN A 487 UNP P07603 EXPRESSION TAG SEQADV 8RYH PHE A 488 UNP P07603 EXPRESSION TAG SEQADV 8RYH GLU A 489 UNP P07603 EXPRESSION TAG SEQADV 8RYH LYS A 490 UNP P07603 EXPRESSION TAG SEQRES 1 A 490 MET SER ARG THR VAL MET GLU ARG ILE GLU TYR GLU MET SEQRES 2 A 490 HIS THR PRO ASP PRO LYS ALA ASP PRO ASP LYS LEU HIS SEQRES 3 A 490 PHE VAL GLN ILE ASP GLU ALA LYS CYS ILE GLY CYS ASP SEQRES 4 A 490 THR CYS SER GLN TYR CYS PRO THR ALA ALA ILE PHE GLY SEQRES 5 A 490 GLU MET GLY GLU PRO HIS SER ILE PRO HIS ILE GLU ALA SEQRES 6 A 490 CYS ILE ASN CYS GLY GLN CYS LEU THR HIS CYS PRO GLU SEQRES 7 A 490 ASN ALA ILE TYR GLU ALA GLN SER TRP VAL PRO GLU VAL SEQRES 8 A 490 GLU LYS LYS LEU LYS ASP GLY LYS VAL LYS CYS ILE ALA SEQRES 9 A 490 MET PRO ALA PRO ALA VAL ARG TYR ALA LEU GLY ASP ALA SEQRES 10 A 490 PHE GLY MET PRO VAL GLY SER VAL THR THR GLY LYS MET SEQRES 11 A 490 LEU ALA ALA LEU GLN LYS LEU GLY PHE ALA HIS CYS TRP SEQRES 12 A 490 ASP THR GLU PHE THR ALA ASP VAL THR ILE TRP GLU GLU SEQRES 13 A 490 GLY SER GLU PHE VAL GLU ARG LEU THR LYS LYS SER ASP SEQRES 14 A 490 MET PRO LEU PRO GLN PHE THR SER CYS CYS PRO GLY TRP SEQRES 15 A 490 GLN LYS TYR ALA GLU THR TYR TYR PRO GLU LEU LEU PRO SEQRES 16 A 490 HIS PHE SER THR CYS LYS SER PRO ILE GLY MET ASN GLY SEQRES 17 A 490 ALA LEU ALA LYS THR TYR GLY ALA GLU ARG MET LYS TYR SEQRES 18 A 490 ASP PRO LYS GLN VAL TYR THR VAL SER ILE MET PRO CYS SEQRES 19 A 490 ILE ALA LYS LYS TYR GLU GLY LEU ARG PRO GLU LEU LYS SEQRES 20 A 490 SER SER GLY MET ARG ASP ILE ASP ALA THR LEU THR THR SEQRES 21 A 490 ARG GLU LEU ALA TYR MET ILE LYS LYS ALA GLY ILE ASP SEQRES 22 A 490 PHE ALA LYS LEU PRO ASP GLY LYS ARG ASP SER LEU MET SEQRES 23 A 490 GLY GLU SER THR GLY GLY ALA THR ILE PHE GLY VAL THR SEQRES 24 A 490 GLY GLY VAL MET GLU ALA ALA LEU ARG PHE ALA TYR GLU SEQRES 25 A 490 ALA VAL THR GLY LYS LYS PRO ASP SER TRP ASP PHE LYS SEQRES 26 A 490 ALA VAL ARG GLY LEU ASP GLY ILE LYS GLU ALA THR VAL SEQRES 27 A 490 ASN VAL GLY GLY THR ASP VAL LYS VAL ALA VAL VAL HIS SEQRES 28 A 490 GLY ALA LYS ARG PHE LYS GLN VAL CYS ASP ASP VAL LYS SEQRES 29 A 490 ALA GLY LYS SER PRO TYR HIS PHE ILE GLU TYR MET ALA SEQRES 30 A 490 CYS PRO GLY GLY CYS VAL CYS GLY GLY GLY GLN PRO ARG SEQRES 31 A 490 VAL LYS LEU PRO MET ALA ASP LYS ALA ARG GLU ALA ARG SEQRES 32 A 490 ILE ASN GLY VAL TYR GLY ALA ASP ALA LYS PHE PRO VAL SEQRES 33 A 490 ARG ALA SER GLN ASP ASN THR GLN VAL LYS ALA LEU TYR SEQRES 34 A 490 LYS SER TYR LEU GLU LYS PRO LEU GLY HIS LYS SER HIS SEQRES 35 A 490 ASP LEU LEU HIS THR HIS TRP PHE ASP LYS SER LYS GLY SEQRES 36 A 490 VAL LYS GLU LEU THR THR ALA GLY LYS LEU PRO ASN PRO SEQRES 37 A 490 ARG ALA SER GLU PHE GLU GLY PRO TYR PRO TYR GLU SER SEQRES 38 A 490 ALA TRP SER HIS PRO GLN PHE GLU LYS HET SF4 A 501 8 HET SF4 A 502 8 HET SF4 A 503 8 HET 402 A 504 24 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM 402 DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU- HETNAM 2 402 (IMINODIMETHANETHIOLATATO-1KAPPAS:2KAPPAS)-MU- HETNAM 3 402 (OXOMETHYLIDENE)DIIRON(2+) FORMUL 2 SF4 3(FE4 S4) FORMUL 5 402 C7 H5 FE2 N3 O3 S2 2+ FORMUL 6 HOH *117(H2 O) HELIX 1 AA1 ASP A 21 LEU A 25 5 5 HELIX 2 AA2 THR A 40 TYR A 44 5 5 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 LEU A 95 1 9 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 ALA A 365 1 11 HELIX 22 AC4 GLY A 381 GLY A 385 5 5 HELIX 23 AC5 ARG A 400 PHE A 414 1 15 HELIX 24 AC6 ALA A 418 ASP A 421 5 4 HELIX 25 AC7 ASN A 422 TYR A 432 1 11 HELIX 26 AC8 GLY A 438 HIS A 446 1 9 HELIX 27 AC9 SER A 453 ALA A 462 1 10 HELIX 28 AD1 ARG A 469 GLU A 474 1 6 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 FE1 SF4 A 502 1555 1555 2.28 LINK SG CYS A 38 FE2 SF4 A 502 1555 1555 2.34 LINK SG CYS A 41 FE3 SF4 A 502 1555 1555 2.26 LINK SG CYS A 45 FE2 SF4 A 501 1555 1555 2.26 LINK SG CYS A 66 FE3 SF4 A 501 1555 1555 2.26 LINK SG CYS A 69 FE4 SF4 A 501 1555 1555 2.38 LINK SG CYS A 72 FE1 SF4 A 501 1555 1555 2.26 LINK SG CYS A 76 FE4 SF4 A 502 1555 1555 2.31 LINK SG CYS A 179 FE3 SF4 A 503 1555 1555 2.18 LINK SG CYS A 234 FE1 SF4 A 503 1555 1555 2.20 LINK SG CYS A 378 FE2 SF4 A 503 1555 1555 2.32 LINK SG CYS A 382 FE4 SF4 A 503 1555 1555 2.29 LINK SG CYS A 382 FE1 402 A 504 1555 1555 2.41 CISPEP 1 LEU A 172 PRO A 173 0 -1.14 CISPEP 2 LEU A 465 PRO A 466 0 1.19 CRYST1 106.118 50.603 86.643 90.00 105.33 90.00 C 1 2 1 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 0.009423 0.000000 0.002583 0.00000 SCALE2 0.000000 0.019762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011967 0.00000 CONECT 549 7219 CONECT 586 7220 CONECT 623 7221 CONECT 683 7212 CONECT 992 7213 CONECT 1036 7214 CONECT 1071 7211 CONECT 1133 7222 CONECT 2711 7229 CONECT 3579 7227 CONECT 5778 7228 CONECT 5817 7230 7235 CONECT 7211 1071 7216 7217 7218 CONECT 7212 683 7215 7217 7218 CONECT 7213 992 7215 7216 7218 CONECT 7214 1036 7215 7216 7217 CONECT 7215 7212 7213 7214 CONECT 7216 7211 7213 7214 CONECT 7217 7211 7212 7214 CONECT 7218 7211 7212 7213 CONECT 7219 549 7224 7225 7226 CONECT 7220 586 7223 7225 7226 CONECT 7221 623 7223 7224 7226 CONECT 7222 1133 7223 7224 7225 CONECT 7223 7220 7221 7222 CONECT 7224 7219 7221 7222 CONECT 7225 7219 7220 7222 CONECT 7226 7219 7220 7221 CONECT 7227 3579 7232 7233 7234 CONECT 7228 5778 7231 7233 7234 CONECT 7229 2711 7231 7232 7234 CONECT 7230 5817 7231 7232 7233 CONECT 7231 7228 7229 7230 CONECT 7232 7227 7229 7230 CONECT 7233 7227 7228 7230 CONECT 7234 7227 7228 7229 CONECT 7235 5817 7237 7238 7244 CONECT 7235 7245 7246 CONECT 7236 7237 7238 7246 7247 CONECT 7236 7248 CONECT 7237 7235 7236 7251 CONECT 7238 7235 7236 7249 CONECT 7239 7244 CONECT 7240 7245 CONECT 7241 7246 CONECT 7242 7247 CONECT 7243 7248 CONECT 7244 7235 7239 CONECT 7245 7235 7240 CONECT 7246 7235 7236 7241 CONECT 7247 7236 7242 CONECT 7248 7236 7243 CONECT 7249 7238 7250 7252 7253 CONECT 7250 7249 7251 7254 CONECT 7251 7237 7250 7255 7256 CONECT 7252 7249 CONECT 7253 7249 CONECT 7254 7250 CONECT 7255 7251 CONECT 7256 7251 MASTER 473 0 4 28 12 0 0 6 3760 1 60 38 END