HEADER OXIDOREDUCTASE 17-DEC-15 5FEZ TITLE HYDE FROM T. MARITIMA IN COMPLEX WITH (2R,4R)-MESETDA, 5'- TITLE 2 DEOXYADENOSINE AND METHIONINE 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: 2336; 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, THIAZOLIDINE, 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 5FEZ 1 REMARK REVDAT 2 04-MAY-16 5FEZ 1 JRNL REVDAT 1 06-APR-16 5FEZ 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 72790 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) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.135 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3833 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 278 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2741 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 215 REMARK 3 SOLVENT ATOMS : 502 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.29000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : -1.16000 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): 0.049 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.042 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.796 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3233 ; 0.024 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3164 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4465 ; 2.277 ; 2.094 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7340 ; 1.434 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 5.946 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;34.425 ;23.435 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;11.887 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.393 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 527 ; 0.227 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3441 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 673 ; 0.005 ; 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): 1469 ; 1.673 ; 1.356 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1468 ; 1.673 ; 1.356 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1859 ; 1.811 ; 2.038 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1860 ; 1.811 ; 2.038 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1764 ; 3.135 ; 1.643 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1762 ; 3.135 ; 1.642 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2587 ; 3.494 ; 2.375 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14707 ; 3.758 ;14.862 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14708 ; 3.758 ;14.862 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6393 ; 9.214 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 39 ;32.399 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6759 ; 9.392 ; 5.000 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 5FEZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-14 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 : 76623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 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) : 0.93900 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 (%): 41.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 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 25.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.12500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.12500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.43500 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: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A -9 REMARK 465 TRP A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 PRO A -5 REMARK 465 GLN A -4 REMARK 465 PHE A -3 REMARK 465 GLU A -2 REMARK 465 LYS A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 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 CD NE CZ NH1 NH2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 77 CD CE NZ REMARK 470 GLU A 87 CD OE1 OE2 REMARK 470 LYS A 242 CE NZ REMARK 470 LYS A 309 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 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 NH2 ARG A 12 O HOH A 501 1.52 REMARK 500 NH1 ARG A 17 O HOH A 502 1.67 REMARK 500 O GLU A 314 O HOH A 503 1.82 REMARK 500 O HOH A 910 O HOH A 933 1.84 REMARK 500 O HOH A 826 O HOH A 946 1.85 REMARK 500 O HOH A 594 O HOH A 772 1.89 REMARK 500 O HOH A 523 O HOH A 536 1.90 REMARK 500 CD LYS A 37 O HOH A 666 1.90 REMARK 500 O HOH A 882 O HOH A 936 1.94 REMARK 500 O HOH A 763 O HOH A 828 1.95 REMARK 500 O HOH A 606 O HOH A 923 1.96 REMARK 500 O HOH A 618 O HOH A 784 1.99 REMARK 500 O HOH A 505 O HOH A 746 2.01 REMARK 500 OE1 GLU A 150 O HOH A 504 2.01 REMARK 500 CD LYS A 309 O HOH A 813 2.07 REMARK 500 O HOH A 505 O HOH A 684 2.07 REMARK 500 O HOH A 712 O HOH A 837 2.08 REMARK 500 O HOH A 673 O HOH A 940 2.10 REMARK 500 O HOH A 627 O HOH A 669 2.11 REMARK 500 O HOH A 896 O HOH A 935 2.14 REMARK 500 O HOH A 566 O HOH A 697 2.15 REMARK 500 OE2 GLU A 14 O HOH A 501 2.16 REMARK 500 O HOH A 506 O HOH A 639 2.17 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 786 O HOH A 899 2655 1.94 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 GLU A 22 CD GLU A 22 OE2 0.084 REMARK 500 ARG A 29 CZ ARG A 29 NH1 0.081 REMARK 500 TYR A 46 CZ TYR A 46 CE2 -0.088 REMARK 500 GLU A 241 CD GLU A 241 OE1 -0.069 REMARK 500 GLU A 346 CD GLU A 346 OE1 -0.091 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 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 81 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 94 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ASP A 174 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 300 NE - CZ - NH2 ANGL. DEV. = -4.2 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 43.49 -95.99 REMARK 500 ASN A 78 40.19 -93.17 REMARK 500 GLU A 161 -58.08 75.07 REMARK 500 THR A 175 -158.74 -152.01 REMARK 500 ALA A 196 -153.57 -122.28 REMARK 500 ASN A 288 12.24 -142.37 REMARK 500 TYR A 303 79.05 -111.23 REMARK 500 ASP A 337 -162.86 -128.08 REMARK 500 GLU A 346 -157.14 -140.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 309 10.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 995 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 997 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 998 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 999 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A1000 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A1001 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH A1002 DISTANCE = 7.85 ANGSTROMS 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 SFS A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 SFS A 401 SE4 117.0 REMARK 620 3 SFS A 401 SE3 113.4 105.9 REMARK 620 4 SFS A 401 SE1 105.0 106.3 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SFS A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 SFS A 401 SE4 106.1 REMARK 620 3 SFS A 401 SE2 115.0 108.4 REMARK 620 4 SFS A 401 SE1 115.8 105.4 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SFS A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 70 SG REMARK 620 2 SFS A 401 SE4 108.9 REMARK 620 3 SFS A 401 SE3 118.5 105.4 REMARK 620 4 SFS A 401 SE2 106.5 108.2 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SFS A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 409 N REMARK 620 2 SFS A 401 SE3 96.0 REMARK 620 3 SFS A 401 SE2 160.6 99.2 REMARK 620 4 SFS A 401 SE1 92.8 99.8 96.5 REMARK 620 5 MET A 409 SD 79.5 87.4 89.1 170.1 REMARK 620 6 MET A 409 OXT 68.2 161.5 94.6 90.8 80.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFS 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 5AD A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MET A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9SE A 410 DBREF 5FEZ A 2 348 UNP Q9X0Z6 HYDE_THEMA 2 348 SEQADV 5FEZ MET A -9 UNP Q9X0Z6 INITIATING METHIONINE SEQADV 5FEZ TRP A -8 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ SER A -7 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ HIS A -6 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ PRO A -5 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ GLN A -4 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ PHE A -3 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ GLU A -2 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ LYS A -1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ ALA A 0 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ SER A 1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 5FEZ SER A 311 UNP Q9X0Z6 CYS 311 ENGINEERED MUTATION SEQADV 5FEZ SER A 319 UNP Q9X0Z6 CYS 319 ENGINEERED MUTATION SEQADV 5FEZ SER A 322 UNP Q9X0Z6 CYS 322 ENGINEERED MUTATION SEQRES 1 A 358 MET TRP SER HIS PRO GLN PHE GLU LYS ALA SER THR GLY SEQRES 2 A 358 ARG GLU ILE LEU GLU LYS LEU GLU ARG ARG GLU PHE THR SEQRES 3 A 358 ARG GLU VAL LEU LYS GLU ALA LEU SER ILE ASN ASP ARG SEQRES 4 A 358 GLY PHE ASN GLU ALA LEU PHE LYS LEU ALA ASP GLU ILE SEQRES 5 A 358 ARG ARG LYS TYR VAL GLY ASP GLU VAL HIS ILE ARG ALA SEQRES 6 A 358 ILE ILE GLU PHE SER ASN VAL CYS ARG LYS ASN CYS LEU SEQRES 7 A 358 TYR CYS GLY LEU ARG ARG ASP ASN LYS ASN LEU LYS ARG SEQRES 8 A 358 TYR ARG MET THR PRO GLU GLU ILE VAL GLU ARG ALA ARG SEQRES 9 A 358 LEU ALA VAL GLN PHE GLY ALA LYS THR ILE VAL LEU GLN SEQRES 10 A 358 SER GLY GLU ASP PRO TYR TYR MET PRO ASP VAL ILE SER SEQRES 11 A 358 ASP ILE VAL LYS GLU ILE LYS LYS MET GLY VAL ALA VAL SEQRES 12 A 358 THR LEU SER LEU GLY GLU TRP PRO ARG GLU TYR TYR GLU SEQRES 13 A 358 LYS TRP LYS GLU ALA GLY ALA ASP ARG TYR LEU LEU ARG SEQRES 14 A 358 HIS GLU THR ALA ASN PRO VAL LEU HIS ARG LYS LEU ARG SEQRES 15 A 358 PRO ASP THR SER PHE GLU ASN ARG LEU ASN CYS LEU LEU SEQRES 16 A 358 THR LEU LYS GLU LEU GLY TYR GLU THR GLY ALA GLY SER SEQRES 17 A 358 MET VAL GLY LEU PRO GLY GLN THR ILE ASP ASP LEU VAL SEQRES 18 A 358 ASP ASP LEU LEU PHE LEU LYS GLU HIS ASP PHE ASP MET SEQRES 19 A 358 VAL GLY ILE GLY PRO PHE ILE PRO HIS PRO ASP THR PRO SEQRES 20 A 358 LEU ALA ASN GLU LYS LYS GLY ASP PHE THR LEU THR LEU SEQRES 21 A 358 LYS MET VAL ALA LEU THR ARG ILE LEU LEU PRO ASP SER SEQRES 22 A 358 ASN ILE PRO ALA THR THR ALA MET GLY THR ILE VAL PRO SEQRES 23 A 358 GLY GLY ARG GLU ILE THR LEU ARG CYS GLY ALA ASN VAL SEQRES 24 A 358 ILE MET PRO ASN TRP THR PRO SER PRO TYR ARG GLN LEU SEQRES 25 A 358 TYR GLN LEU TYR PRO GLY LYS ILE SER VAL PHE GLU LYS SEQRES 26 A 358 ASP THR ALA SER ILE PRO SER VAL MET LYS MET ILE GLU SEQRES 27 A 358 LEU LEU GLY ARG LYS PRO GLY ARG ASP TRP GLY GLY ARG SEQRES 28 A 358 LYS ARG VAL PHE GLU THR VAL HET SFS A 401 8 HET CPS A 402 42 HET CPS A 403 42 HET CPS A 404 29 HET CPS A 405 29 HET CPS A 406 50 HET CL A 407 1 HET 5AD A 408 18 HET MET A 409 9 HET 9SE A 410 12 HETNAM SFS FE4-SE4 CLUSTER HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM CL CHLORIDE ION HETNAM 5AD 5'-DEOXYADENOSINE HETNAM MET METHIONINE HETNAM 9SE (2~{R},4~{R})-2-METHYL-1,3-SELENAZOLIDINE-2,4- HETNAM 2 9SE DICARBOXYLIC ACID HETSYN CPS CHAPS FORMUL 2 SFS FE4 SE4 FORMUL 3 CPS 5(C32 H58 N2 O7 S) FORMUL 8 CL CL 1- FORMUL 9 5AD C10 H13 N5 O3 FORMUL 10 MET C5 H11 N O2 S FORMUL 11 9SE C6 H9 N O4 SE FORMUL 12 HOH *502(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 GLY A 152 1 12 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 ARG A 155 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 ARG A 155 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 SFS A 401 1555 1555 2.30 LINK SG CYS A 67 FE3 SFS A 401 1555 1555 2.34 LINK SG CYS A 70 FE1 SFS A 401 1555 1555 2.26 LINK FE4 SFS A 401 N MET A 409 1555 1555 2.25 LINK FE4 SFS A 401 SD MET A 409 1555 1555 2.63 LINK FE4 SFS A 401 OXT MET A 409 1555 1555 2.26 CISPEP 1 MET A 115 PRO A 116 0 -4.18 CISPEP 2 SER A 297 PRO A 298 0 7.90 CISPEP 3 SER A 297 PRO A 298 0 9.00 SITE 1 AC1 4 CYS A 63 CYS A 67 CYS A 70 MET A 409 SITE 1 AC2 17 GLN A 98 PHE A 99 GLY A 100 GLY A 277 SITE 2 AC2 17 GLU A 280 ARG A 284 MET A 324 LEU A 330 SITE 3 AC2 17 CPS A 405 CPS A 406 HOH A 581 HOH A 642 SITE 4 AC2 17 HOH A 686 HOH A 694 HOH A 776 HOH A 779 SITE 5 AC2 17 HOH A 967 SITE 1 AC3 14 LYS A 37 ASP A 40 LYS A 170 ARG A 284 SITE 2 AC3 14 SER A 297 LYS A 315 ASP A 316 THR A 317 SITE 3 AC3 14 HOH A 575 HOH A 609 HOH A 628 HOH A 666 SITE 4 AC3 14 HOH A 753 HOH A 915 SITE 1 AC4 10 ARG A 29 GLU A 33 PHE A 246 THR A 247 SITE 2 AC4 10 LEU A 250 CPS A 405 HOH A 516 HOH A 676 SITE 3 AC4 10 HOH A 718 HOH A 993 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 525 SITE 3 AC5 12 HOH A 643 HOH A 645 HOH A 677 HOH A 737 SITE 1 AC6 18 LYS A 128 PRO A 321 MET A 324 LYS A 325 SITE 2 AC6 18 GLU A 328 TRP A 338 CPS A 402 CPS A 405 SITE 3 AC6 18 HOH A 649 HOH A 665 HOH A 670 HOH A 723 SITE 4 AC6 18 HOH A 775 HOH A 820 HOH A 914 HOH A 968 SITE 5 AC6 18 HOH A 986 HOH A 997 SITE 1 AC7 4 ARG A 54 THR A 134 ARG A 155 HOH A 938 SITE 1 AC8 12 TYR A 69 ARG A 159 GLU A 161 MET A 199 SITE 2 AC8 12 PRO A 229 ILE A 231 LEU A 305 TYR A 306 SITE 3 AC8 12 MET A 409 9SE A 410 HOH A 633 HOH A 689 SITE 1 AC9 10 SER A 108 SER A 136 GLY A 138 ARG A 180 SITE 2 AC9 10 TYR A 303 SFS A 401 5AD A 408 HOH A 569 SITE 3 AC9 10 HOH A 630 HOH A 633 SITE 1 AD1 13 ILE A 56 ARG A 159 THR A 268 THR A 269 SITE 2 AD1 13 ALA A 270 MET A 291 TYR A 306 5AD A 408 SITE 3 AD1 13 HOH A 526 HOH A 647 HOH A 650 HOH A 685 SITE 4 AD1 13 HOH A 749 CRYST1 50.800 78.870 86.250 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 0.019685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011594 0.00000