HEADER OXIDOREDUCTASE 07-FEB-24 8RXJ TITLE DESULFOVIBRIO DESULFURICANS [FEFE] HYDROGENASE C178A MUTANT IN HINACT- TITLE 2 LIKE STATE DERIVATIZED WITH KRYPTON 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: (DELTA)ISCR; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS; SOURCE 10 ORGANISM_TAXID: 876; SOURCE 11 GENE: HYDB, DVU_1770; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_VARIANT: (DELTA)ISCR KEYWDS [FEFE] HYDROGENASE, INHIBITOR, IRON-SULFUR CLUSTER, GAS CHANNEL, KEYWDS 2 KRYPTON, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BIKBAEV,T.HARAND,L.SCHEUENSTUHL,P.CARPENTIER,I.SPAN REVDAT 1 19-FEB-25 8RXJ 0 JRNL AUTH K.BIKBAEV,T.HARAND,L.SCHEUENSTUHL,P.CARPENTIER,M.A.MARTINI, JRNL AUTH 2 J.A.BIRRELL,I.SPAN JRNL TITL KRYPTON DERIVATIZATION OF [FEFE] HYDROGENASE FROM JRNL TITL 2 DESULFOVIBRIO DESULFURICANS REVEALS ITS GAS CHANNEL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 60676 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) : 0.158 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.208 REMARK 3 FREE R VALUE TEST SET COUNT : 3160 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) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3830 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 191 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.53500 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : -1.06500 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.644 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3847 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3512 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5250 ; 2.008 ; 1.839 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8137 ; 0.628 ; 1.743 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 6.352 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 8.281 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 607 ;13.102 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4415 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 797 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 859 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 62 ; 0.267 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1904 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.120 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.093 ; 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): 1944 ; 1.713 ; 2.054 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1943 ; 1.713 ; 2.054 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2430 ; 2.417 ; 3.688 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2431 ; 2.417 ; 3.688 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1903 ; 2.503 ; 2.242 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1904 ; 2.502 ; 2.243 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2776 ; 3.657 ; 4.023 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2777 ; 3.656 ; 4.024 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 8RXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.861 REMARK 200 MONOCHROMATOR : SILICON (1 1 1) CHANNEL-CUT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60747 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.507 REMARK 200 RESOLUTION RANGE LOW (A) : 43.503 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 43.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 31.70 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LITHIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 35 % 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: 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 24.68800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.44450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.44450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.46550 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: 10320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 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 MET A 1 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 19 CE NZ REMARK 480 LYS A 24 NZ REMARK 480 LYS A 34 NZ REMARK 480 GLU A 53 CD OE1 OE2 REMARK 480 LYS A 93 CD CE NZ REMARK 480 LYS A 96 CE NZ REMARK 480 LYS A 99 CD CE NZ REMARK 480 GLN A 135 OE1 REMARK 480 LYS A 136 NZ REMARK 480 THR A 165 O REMARK 480 LYS A 166 CG CD CE NZ 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 281 CG CD CE NZ REMARK 480 LYS A 317 CB CG 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 346 CE 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 HZ2 LYS A 19 O HOH A 601 1.17 REMARK 500 HZ3 LYS A 201 HG SER A 248 1.18 REMARK 500 HG CYS A 382 FE1 402 A 511 1.24 REMARK 500 HG1 THR A 299 HZ3 LYS A 334 1.31 REMARK 500 H LYS A 346 HD1 HIS A 371 1.34 REMARK 500 FE2 402 A 511 C CYN A 515 1.85 REMARK 500 OE1 GLN B 38 O HOH B 201 1.86 REMARK 500 NZ LYS A 19 O HOH A 601 1.90 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 HG1 THR A 343 H2 VAL B 36 3444 1.25 REMARK 500 HG3 LYS A 166 OD1 ASP B 41 3444 1.57 REMARK 500 CG LYS A 166 OD1 ASP B 41 3444 2.14 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 367 C LYS A 367 O -0.134 REMARK 500 GLN B 38 CD GLN B 38 NE2 0.248 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 ASP A 320 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 GLN B 38 OE1 - CD - NE2 ANGL. DEV. = -19.2 DEGREES REMARK 500 GLN B 38 CG - CD - OE1 ANGL. DEV. = 12.6 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 ARG A 8 -12.18 78.58 REMARK 500 ASP A 39 9.22 84.23 REMARK 500 THR A 213 -81.92 -123.34 REMARK 500 LYS A 247 41.16 -145.94 REMARK 500 TYR B 75 -60.33 -143.65 REMARK 500 GLU B 77 -56.08 80.12 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 8 0.09 SIDE CHAIN REMARK 500 ARG A 243 0.09 SIDE CHAIN REMARK 500 ASP A 320 0.09 SIDE CHAIN REMARK 500 ASP A 344 0.09 SIDE CHAIN REMARK 500 GLN B 38 0.11 SIDE CHAIN REMARK 500 GLU B 101 0.10 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 514 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 SG REMARK 620 2 SF4 A 514 S2 123.0 REMARK 620 3 SF4 A 514 S3 102.6 104.9 REMARK 620 4 SF4 A 514 S4 115.9 103.7 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 514 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 SF4 A 514 S1 99.5 REMARK 620 3 SF4 A 514 S2 115.6 108.0 REMARK 620 4 SF4 A 514 S3 126.4 104.7 101.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 514 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 SF4 A 514 S1 110.7 REMARK 620 3 SF4 A 514 S3 106.3 108.0 REMARK 620 4 SF4 A 514 S4 119.0 106.1 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 513 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 513 S1 114.7 REMARK 620 3 SF4 A 513 S2 111.7 103.2 REMARK 620 4 SF4 A 513 S3 117.6 103.5 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 513 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 513 S1 117.2 REMARK 620 3 SF4 A 513 S3 120.5 104.4 REMARK 620 4 SF4 A 513 S4 104.8 103.8 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 513 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 SF4 A 513 S1 126.4 REMARK 620 3 SF4 A 513 S2 100.4 103.2 REMARK 620 4 SF4 A 513 S4 119.0 101.5 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 513 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 SF4 A 513 S2 109.4 REMARK 620 3 SF4 A 513 S3 124.2 104.3 REMARK 620 4 SF4 A 513 S4 111.3 104.0 101.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 514 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 SF4 A 514 S1 111.3 REMARK 620 3 SF4 A 514 S2 113.4 107.2 REMARK 620 4 SF4 A 514 S4 116.6 105.1 102.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 512 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 179 SG REMARK 620 2 SF4 A 512 S1 114.2 REMARK 620 3 SF4 A 512 S3 117.4 104.0 REMARK 620 4 SF4 A 512 S4 109.8 104.4 105.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 512 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 SF4 A 512 S1 122.0 REMARK 620 3 SF4 A 512 S2 105.3 105.4 REMARK 620 4 SF4 A 512 S4 110.4 104.5 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 512 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 378 SG REMARK 620 2 SF4 A 512 S2 116.0 REMARK 620 3 SF4 A 512 S3 118.1 102.3 REMARK 620 4 SF4 A 512 S4 105.9 108.2 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 402 A 511 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 402 A 511 S1 94.0 REMARK 620 3 402 A 511 S2 97.3 85.3 REMARK 620 4 402 A 511 C3 90.0 174.9 91.0 REMARK 620 5 402 A 511 C4 91.5 87.6 169.1 95.5 REMARK 620 6 402 A 511 C5 175.6 89.3 85.9 86.9 85.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 512 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 382 SG REMARK 620 2 SF4 A 512 S1 104.8 REMARK 620 3 SF4 A 512 S2 117.9 105.5 REMARK 620 4 SF4 A 512 S3 118.3 105.5 103.6 REMARK 620 N 1 2 3 DBREF 8RXJ A 1 397 UNP P07598 PHFL_DESVH 1 397 DBREF 8RXJ B 36 123 UNP P07603 PHFS_DESVH 36 123 SEQADV 8RXJ ALA A 178 UNP P07598 CYS 178 ENGINEERED MUTATION SEQADV 8RXJ TRP A 398 UNP P07598 EXPRESSION TAG SEQADV 8RXJ SER A 399 UNP P07598 EXPRESSION TAG SEQADV 8RXJ HIS A 400 UNP P07598 EXPRESSION TAG SEQADV 8RXJ PRO A 401 UNP P07598 EXPRESSION TAG SEQADV 8RXJ GLN A 402 UNP P07598 EXPRESSION TAG SEQADV 8RXJ PHE A 403 UNP P07598 EXPRESSION TAG SEQADV 8RXJ GLU A 404 UNP P07598 EXPRESSION TAG SEQADV 8RXJ LYS A 405 UNP P07598 EXPRESSION TAG 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 ALA 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 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 KR A 501 1 HET KR A 502 1 HET KR A 503 1 HET KR A 504 1 HET KR A 505 1 HET KR A 506 1 HET KR A 507 1 HET KR A 508 1 HET KR A 509 1 HET KR A 510 1 HET 402 A 511 24 HET SF4 A 512 8 HET SF4 A 513 8 HET SF4 A 514 8 HET CYN A 515 2 HET TOE A 516 26 HETNAM KR KRYPTON 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 HETNAM CYN CYANIDE ION HETNAM TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL FORMUL 3 KR 10(KR) FORMUL 13 402 C7 H5 FE2 N3 O3 S2 2+ FORMUL 14 SF4 3(FE4 S4) FORMUL 17 CYN C N 1- FORMUL 18 TOE C7 H16 O4 FORMUL 19 HOH *220(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 CYS A 72 CYS A 76 5 5 HELIX 5 AA5 TRP A 87 ASP A 97 1 11 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 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 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 VAL A 338 O VAL A 345 LINK SG CYS A 35 FE1 SF4 A 514 1555 1555 2.25 LINK SG CYS A 38 FE4 SF4 A 514 1555 1555 2.31 LINK SG CYS A 41 FE2 SF4 A 514 1555 1555 2.36 LINK SG CYS A 45 FE4 SF4 A 513 1555 1555 2.30 LINK SG CYS A 66 FE2 SF4 A 513 1555 1555 2.29 LINK SG CYS A 69 FE3 SF4 A 513 1555 1555 2.30 LINK SG CYS A 72 FE1 SF4 A 513 1555 1555 2.29 LINK SG CYS A 76 FE3 SF4 A 514 1555 1555 2.29 LINK SG CYS A 179 FE2 SF4 A 512 1555 1555 2.27 LINK SG CYS A 234 FE3 SF4 A 512 1555 1555 2.23 LINK SG CYS A 378 FE1 SF4 A 512 1555 1555 2.30 LINK SG CYS A 382 FE1 402 A 511 1555 1555 2.39 LINK SG CYS A 382 FE4 SF4 A 512 1555 1555 2.36 CISPEP 1 LEU A 172 PRO A 173 0 -2.83 CISPEP 2 LEU B 108 PRO B 109 0 -0.73 CRYST1 49.376 86.931 88.889 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 0.020253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011250 0.00000