HEADER OXIDOREDUCTASE 17-DEC-15 5FF2 TITLE HYDE FROM T. MARITIMA IN COMPLEX WITH (2R,4R)-TDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: [FEFE] HYDROGENASE MATURASE SUBUNIT HYDE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.8.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 GENE: TM_1269, THEMA_07990, TMARI_1274; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RADICAL SAM ENZYME, COMPLEX, FEFE-HYDROGENASE MATURASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.ROHAC,P.AMARA,A.BENJDIA,L.MARTIN,P.RUFFIE,A.FAVIER,O.BERTEAU, AUTHOR 2 J.M.MOUESCA,J.C.FONTECILLA-CAMPS,Y.NICOLET REVDAT 3 10-JAN-24 5FF2 1 REMARK REVDAT 2 04-MAY-16 5FF2 1 JRNL REVDAT 1 06-APR-16 5FF2 0 JRNL AUTH R.ROHAC,P.AMARA,A.BENJDIA,L.MARTIN,P.RUFFIE,A.FAVIER, JRNL AUTH 2 O.BERTEAU,J.M.MOUESCA,J.C.FONTECILLA-CAMPS,Y.NICOLET JRNL TITL CARBON-SULFUR BOND-FORMING REACTION CATALYSED BY THE RADICAL JRNL TITL 2 SAM ENZYME HYDE. JRNL REF NAT.CHEM. V. 8 491 2016 JRNL REFN ESSN 1755-4349 JRNL PMID 27102684 JRNL DOI 10.1038/NCHEM.2490 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 56772 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3009 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4079 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2742 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 212 REMARK 3 SOLVENT ATOMS : 447 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -1.04000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.473 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3211 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3136 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4428 ; 2.296 ; 2.078 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7278 ; 1.261 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 6.143 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;35.188 ;23.209 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 539 ;12.680 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 525 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3379 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 668 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1448 ; 1.682 ; 1.567 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1447 ; 1.682 ; 1.567 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1822 ; 2.286 ; 2.346 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1823 ; 2.285 ; 2.347 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1763 ; 2.744 ; 1.903 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1764 ; 2.743 ; 1.903 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2583 ; 4.014 ; 2.764 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14287 ; 6.144 ;16.554 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14286 ; 6.144 ;16.553 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5FF2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59781 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.68300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3IIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, LITHIUM SULFATE, CHAPS, REMARK 280 TRISHCL, VAPOR DIFFUSION, HANGING 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 25.61500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.61500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.54500 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 TOTAL BURIED SURFACE AREA: 3060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL 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 VAL A 348 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 9 CE NZ REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 LYS A 37 CE NZ REMARK 470 LYS A 80 CD CE NZ REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 LYS A 188 CD CE NZ REMARK 470 LYS A 242 CE NZ REMARK 470 GLN A 304 CG CD OE1 NE2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 315 CE NZ REMARK 470 LYS A 333 CE NZ REMARK 470 ARG A 336 CD NE CZ NH1 NH2 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 37 CD 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 CD LYS A 37 O HOH A 716 1.67 REMARK 500 O HOH A 617 O HOH A 736 1.78 REMARK 500 O HOH A 772 O HOH A 822 1.83 REMARK 500 O HOH A 873 O HOH A 922 1.89 REMARK 500 O HOH A 764 O HOH A 916 1.91 REMARK 500 CB LYS A 309 O HOH A 860 1.93 REMARK 500 O HOH A 826 O HOH A 855 1.96 REMARK 500 O HOH A 581 O HOH A 928 2.03 REMARK 500 O HOH A 791 O HOH A 869 2.05 REMARK 500 O HOH A 523 O HOH A 790 2.09 REMARK 500 NH2 ARG A 44 O HOH A 501 2.09 REMARK 500 O HOH A 719 O HOH A 900 2.11 REMARK 500 O HOH A 942 O HOH A 946 2.14 REMARK 500 O HOH A 681 O HOH A 802 2.16 REMARK 500 CZ ARG A 44 O HOH A 501 2.16 REMARK 500 O HOH A 867 O HOH A 894 2.17 REMARK 500 O HOH A 550 O HOH A 807 2.18 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 O HOH A 725 O HOH A 881 2655 2.08 REMARK 500 O HOH A 842 O HOH A 872 4555 2.09 REMARK 500 O HOH A 604 O HOH A 858 2655 2.17 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 ARG A 92 CZ ARG A 92 NH1 0.079 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 29 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 113 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 MET A 129 CG - SD - CE ANGL. DEV. = -23.1 DEGREES REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 212 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 MET A 291 CG - SD - CE ANGL. DEV. = -18.4 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ASN A 78 37.74 -94.60 REMARK 500 ASN A 78 30.82 -89.03 REMARK 500 GLU A 161 -59.43 78.64 REMARK 500 THR A 175 -159.63 -151.93 REMARK 500 ALA A 196 -154.41 -123.25 REMARK 500 ASN A 288 11.43 -143.93 REMARK 500 GLN A 304 79.36 -117.54 REMARK 500 CYS A 311 -2.54 78.14 REMARK 500 ASP A 337 -159.90 -132.45 REMARK 500 GLU A 346 -158.39 -121.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CPS A 404 REMARK 610 CPS A 405 REMARK 610 CPS A 406 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 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 SF4 A 401 S1 105.4 REMARK 620 3 SF4 A 401 S3 116.9 106.4 REMARK 620 4 SF4 A 401 S4 118.9 103.9 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 SF4 A 401 S1 115.8 REMARK 620 3 SF4 A 401 S2 117.4 103.7 REMARK 620 4 SF4 A 401 S4 108.4 103.4 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 70 SG REMARK 620 2 SF4 A 401 S2 110.8 REMARK 620 3 SF4 A 401 S3 118.6 106.7 REMARK 620 4 SF4 A 401 S4 108.7 105.1 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAH A 408 N REMARK 620 2 SF4 A 401 S1 98.6 REMARK 620 3 SF4 A 401 S2 156.9 98.4 REMARK 620 4 SF4 A 401 S3 92.5 101.3 99.4 REMARK 620 5 SAH A 408 OXT 70.2 95.2 92.7 157.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5XB A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H2S A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H2S A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IIX RELATED DB: PDB REMARK 900 RELATED ID: 3IIZ RELATED DB: PDB REMARK 900 RELATED ID: 5FEP RELATED DB: PDB REMARK 900 RELATED ID: 5FES RELATED DB: PDB REMARK 900 RELATED ID: 5FEW RELATED DB: PDB REMARK 900 RELATED ID: 5FEX RELATED DB: PDB REMARK 900 RELATED ID: 5FEZ RELATED DB: PDB REMARK 900 RELATED ID: 5FF0 RELATED DB: PDB DBREF 5FF2 A 1 348 UNP Q9X0Z6 HYDE_THEMA 1 348 SEQRES 1 A 348 MET THR GLY ARG GLU ILE LEU GLU LYS LEU GLU ARG ARG SEQRES 2 A 348 GLU PHE THR ARG GLU VAL LEU LYS GLU ALA LEU SER ILE SEQRES 3 A 348 ASN ASP ARG GLY PHE ASN GLU ALA LEU PHE LYS LEU ALA SEQRES 4 A 348 ASP GLU ILE ARG ARG LYS TYR VAL GLY ASP GLU VAL HIS SEQRES 5 A 348 ILE ARG ALA ILE ILE GLU PHE SER ASN VAL CYS ARG LYS SEQRES 6 A 348 ASN CYS LEU TYR CYS GLY LEU ARG ARG ASP ASN LYS ASN SEQRES 7 A 348 LEU LYS ARG TYR ARG MET THR PRO GLU GLU ILE VAL GLU SEQRES 8 A 348 ARG ALA ARG LEU ALA VAL GLN PHE GLY ALA LYS THR ILE SEQRES 9 A 348 VAL LEU GLN SER GLY GLU ASP PRO TYR TYR MET PRO ASP SEQRES 10 A 348 VAL ILE SER ASP ILE VAL LYS GLU ILE LYS LYS MET GLY SEQRES 11 A 348 VAL ALA VAL THR LEU SER LEU GLY GLU TRP PRO ARG GLU SEQRES 12 A 348 TYR TYR GLU LYS TRP LYS GLU ALA GLY ALA ASP ARG TYR SEQRES 13 A 348 LEU LEU ARG HIS GLU THR ALA ASN PRO VAL LEU HIS ARG SEQRES 14 A 348 LYS LEU ARG PRO ASP THR SER PHE GLU ASN ARG LEU ASN SEQRES 15 A 348 CYS LEU LEU THR LEU LYS GLU LEU GLY TYR GLU THR GLY SEQRES 16 A 348 ALA GLY SER MET VAL GLY LEU PRO GLY GLN THR ILE ASP SEQRES 17 A 348 ASP LEU VAL ASP ASP LEU LEU PHE LEU LYS GLU HIS ASP SEQRES 18 A 348 PHE ASP MET VAL GLY ILE GLY PRO PHE ILE PRO HIS PRO SEQRES 19 A 348 ASP THR PRO LEU ALA ASN GLU LYS LYS GLY ASP PHE THR SEQRES 20 A 348 LEU THR LEU LYS MET VAL ALA LEU THR ARG ILE LEU LEU SEQRES 21 A 348 PRO ASP SER ASN ILE PRO ALA THR THR ALA MET GLY THR SEQRES 22 A 348 ILE VAL PRO GLY GLY ARG GLU ILE THR LEU ARG CYS GLY SEQRES 23 A 348 ALA ASN VAL ILE MET PRO ASN TRP THR PRO SER PRO TYR SEQRES 24 A 348 ARG GLN LEU TYR GLN LEU TYR PRO GLY LYS ILE CYS VAL SEQRES 25 A 348 PHE GLU LYS ASP THR ALA CYS ILE PRO CYS VAL MET LYS SEQRES 26 A 348 MET ILE GLU LEU LEU GLY ARG LYS PRO GLY ARG ASP TRP SEQRES 27 A 348 GLY GLY ARG LYS ARG VAL PHE GLU THR VAL HET SF4 A 401 8 HET CPS A 402 42 HET CPS A 403 42 HET CPS A 404 29 HET CPS A 405 26 HET CPS A 406 50 HET CL A 407 1 HET SAH A 408 26 HET 5XB A 409 11 HET H2S A 410 1 HET H2S A 411 1 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM CL CHLORIDE ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM 5XB (2~{R},4~{R})-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC ACID HETNAM H2S HYDROSULFURIC ACID HETSYN CPS CHAPS HETSYN H2S HYDROGEN SULFIDE FORMUL 2 SF4 FE4 S4 FORMUL 3 CPS 5(C32 H58 N2 O7 S) FORMUL 8 CL CL 1- FORMUL 9 SAH C14 H20 N6 O5 S FORMUL 10 5XB C5 H7 N O4 S FORMUL 11 H2S 2(H2 S) FORMUL 13 HOH *447(H2 O) HELIX 1 AA1 THR A 2 ARG A 12 1 11 HELIX 2 AA2 THR A 16 ILE A 26 1 11 HELIX 3 AA3 ASP A 28 GLY A 48 1 21 HELIX 4 AA4 THR A 85 PHE A 99 1 15 HELIX 5 AA5 ASP A 111 MET A 115 5 5 HELIX 6 AA6 PRO A 116 LYS A 128 1 13 HELIX 7 AA7 PRO A 141 ALA A 151 1 11 HELIX 8 AA8 ASN A 164 ARG A 172 1 9 HELIX 9 AA9 SER A 176 LEU A 190 1 15 HELIX 10 AB1 THR A 206 ASP A 221 1 16 HELIX 11 AB2 ASP A 245 LEU A 260 1 16 HELIX 12 AB3 THR A 268 VAL A 275 1 8 HELIX 13 AB4 GLY A 277 ARG A 284 1 8 HELIX 14 AB5 TYR A 299 TYR A 303 5 5 HELIX 15 AB6 ALA A 318 LEU A 330 1 13 SHEET 1 AA1 7 MET A 224 PRO A 229 0 SHEET 2 AA1 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226 SHEET 3 AA1 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195 SHEET 4 AA1 7 ALA A 132 SER A 136 1 N LEU A 135 O LEU A 157 SHEET 5 AA1 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134 SHEET 6 AA1 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 AA1 7 VAL A 289 ILE A 290 1 O ILE A 290 N HIS A 52 SHEET 1 AA2 7 MET A 224 PRO A 229 0 SHEET 2 AA2 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226 SHEET 3 AA2 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195 SHEET 4 AA2 7 ALA A 132 SER A 136 1 N LEU A 135 O LEU A 157 SHEET 5 AA2 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134 SHEET 6 AA2 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 AA2 7 LYS A 333 PRO A 334 1 O LYS A 333 N VAL A 51 LINK SG CYS A 63 FE2 SF4 A 401 1555 1555 2.26 LINK SG CYS A 67 FE3 SF4 A 401 1555 1555 2.33 LINK SG CYS A 70 FE1 SF4 A 401 1555 1555 2.29 LINK FE4 SF4 A 401 N SAH A 408 1555 1555 2.31 LINK FE4 SF4 A 401 OXT SAH A 408 1555 1555 2.33 CISPEP 1 MET A 115 PRO A 116 0 -5.60 CISPEP 2 SER A 297 PRO A 298 0 8.14 SITE 1 AC1 4 CYS A 63 CYS A 67 CYS A 70 SAH A 408 SITE 1 AC2 19 GLN A 98 PHE A 99 GLY A 100 PRO A 276 SITE 2 AC2 19 GLY A 277 GLU A 280 ARG A 284 MET A 324 SITE 3 AC2 19 LEU A 330 CPS A 405 CPS A 406 HOH A 540 SITE 4 AC2 19 HOH A 543 HOH A 561 HOH A 571 HOH A 599 SITE 5 AC2 19 HOH A 657 HOH A 662 HOH A 776 SITE 1 AC3 17 LYS A 37 ASP A 40 LYS A 170 ARG A 284 SITE 2 AC3 17 SER A 297 LYS A 315 ASP A 316 THR A 317 SITE 3 AC3 17 HOH A 603 HOH A 616 HOH A 623 HOH A 648 SITE 4 AC3 17 HOH A 653 HOH A 737 HOH A 803 HOH A 840 SITE 5 AC3 17 HOH A 903 SITE 1 AC4 8 ARG A 29 GLU A 33 THR A 247 CPS A 405 SITE 2 AC4 8 HOH A 521 HOH A 614 HOH A 615 HOH A 687 SITE 1 AC5 12 ARG A 29 LYS A 315 THR A 317 ALA A 318 SITE 2 AC5 12 CPS A 402 CPS A 404 CPS A 406 HOH A 626 SITE 3 AC5 12 HOH A 679 HOH A 743 HOH A 755 HOH A 757 SITE 1 AC6 15 LYS A 128 PRO A 321 MET A 324 GLU A 328 SITE 2 AC6 15 CPS A 402 CPS A 405 HOH A 505 HOH A 551 SITE 3 AC6 15 HOH A 571 HOH A 585 HOH A 597 HOH A 670 SITE 4 AC6 15 HOH A 702 HOH A 721 HOH A 842 SITE 1 AC7 3 ARG A 54 THR A 134 ARG A 155 SITE 1 AC8 17 TYR A 69 SER A 108 ARG A 159 GLU A 161 SITE 2 AC8 17 ARG A 180 MET A 199 PRO A 229 ILE A 231 SITE 3 AC8 17 TYR A 303 LEU A 305 TYR A 306 SF4 A 401 SITE 4 AC8 17 HOH A 589 HOH A 608 HOH A 629 HOH A 633 SITE 5 AC8 17 HOH A 739 SITE 1 AC9 13 GLN A 107 ARG A 159 GLY A 226 THR A 268 SITE 2 AC9 13 THR A 269 ALA A 270 MET A 291 TYR A 306 SITE 3 AC9 13 HOH A 535 HOH A 547 HOH A 607 HOH A 768 SITE 4 AC9 13 HOH A 800 SITE 1 AD1 2 CYS A 311 CYS A 319 SITE 1 AD2 2 CYS A 322 HOH A 915 CRYST1 51.230 79.090 86.100 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 0.019520 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011614 0.00000