HEADER OXIDOREDUCTASE 05-MAY-04 1VYS TITLE STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102Y MUTANT AND TITLE 2 COMPLEXED WITH PICRIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENTAERYTHRITOL TETRANITRATE REDUCTASE; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: 2,4,6 TRINITROPHENOL IS BOUND IN THE ACTIVE SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER CLOACAE; SOURCE 3 ORGANISM_TAXID: 550; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PONR1; SOURCE 8 OTHER_DETAILS: NCBI U68759. RECOMBINANT KEYWDS FLAVOENZYME, EXPLOSIVE DEGRADATION, STEROID BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.BARNA,P.C.E.MOODY REVDAT 7 13-DEC-23 1VYS 1 REMARK REVDAT 6 24-OCT-18 1VYS 1 SOURCE REVDAT 5 24-APR-13 1VYS 1 HEADER TITLE KEYWDS REMARK REVDAT 5 2 1 VERSN DBREF REVDAT 4 25-APR-12 1VYS 1 TITLE REMARK FORMUL REVDAT 3 24-FEB-09 1VYS 1 VERSN REVDAT 2 16-JUL-04 1VYS 1 JRNL REVDAT 1 26-MAY-04 1VYS 0 JRNL AUTH H.KHAN,T.BARNA,R.HARRIS,N.BRUCE,I.BARSUKOV,A.MUNRO, JRNL AUTH 2 P.C.E.MOODY,N.SCRUTTON JRNL TITL ATOMIC RESOLUTION STRUCTURES AND SOLUTION BEHAVIOR OF JRNL TITL 2 ENZYME-SUBSTRATE COMPLEXES OF ENTEROBACTER CLOACAE PB2 JRNL TITL 3 PENTAERYTHRITOL TETRANITRATE REDUCTASE: MULTIPLE JRNL TITL 4 CONFORMATIONAL STATES AND IMPLICATIONS FOR THE MECHANISM OF JRNL TITL 5 NITROAROMATIC EXPLOSIVE DEGRADATION JRNL REF J.BIOL.CHEM. V. 279 30563 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15128738 JRNL DOI 10.1074/JBC.M403541200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.M.BARNA,H.KHAN,N.C.BRUCE,I.BARSUKOV,N.S.SCRUTTON,P.C.MOODY REMARK 1 TITL CRYSTAL STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE: REMARK 1 TITL 2 "FLIPPED" BINDING GEOMETRIES FOR STEROID SUBSTRATES IN REMARK 1 TITL 3 DIFFERENT REDOX STATES OF THE ENZYME REMARK 1 REF J.MOL.BIOL. V. 310 433 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11428899 REMARK 1 DOI 10.1006/JMBI.2001.4779 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.C.E.MOODY,N.SHIKOTRA,C.E.FRENCH,N.C.BRUCE,N.S.SCRUTTON REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DIFFRACTION STUDIES OF REMARK 1 TITL 2 PENTAERYTHRITOL TETRANITRATE REDUCTASE FROM ENTEROBACTER REMARK 1 TITL 3 CLOACAE PB2. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 675 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 9761872 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 27293 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1404 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2753 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 604 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.03000 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): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.467 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290014898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29340 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1GVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.20 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 28.29550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.30150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.30150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.29550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.16500 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: X 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION IN CHAIN X, TRP 103 TO TYR 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 ILE X 31 CD1 REMARK 470 ILE X 36 CD1 REMARK 470 ILE X 54 CD1 REMARK 470 ILE X 55 CD1 REMARK 470 ILE X 61 CD1 REMARK 470 ILE X 80 CD1 REMARK 470 ILE X 86 CD1 REMARK 470 ILE X 97 CD1 REMARK 470 ILE X 107 CD1 REMARK 470 ILE X 112 CD1 REMARK 470 ILE X 141 CD1 REMARK 470 ILE X 156 CD1 REMARK 470 ILE X 159 CD1 REMARK 470 ILE X 230 CD1 REMARK 470 ILE X 232 CD1 REMARK 470 ILE X 237 CD1 REMARK 470 ILE X 257 CD1 REMARK 470 ILE X 265 CD1 REMARK 470 ILE X 297 CD1 REMARK 470 ILE X 298 CD1 REMARK 470 ILE X 312 CD1 REMARK 470 ILE X 317 CD1 REMARK 470 ILE X 327 CD1 REMARK 470 LEU X 364 O 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 CG1 ILE X 55 O HOH X 2355 1.69 REMARK 500 CG1 ILE X 107 O HOH X 2361 1.70 REMARK 500 CG1 ILE X 61 O HOH X 2330 1.71 REMARK 500 CG1 ILE X 54 O HOH X 2109 1.74 REMARK 500 CG1 ILE X 80 O HOH X 2174 1.77 REMARK 500 CG1 ILE X 297 O HOH X 2502 1.78 REMARK 500 CG1 ILE X 230 O HOH X 2417 1.82 REMARK 500 CG1 ILE X 31 O HOH X 2042 1.89 REMARK 500 NZ LYS X 279 O HOH X 2484 2.12 REMARK 500 OE1 GLN X 287 O HOH X 2498 2.15 REMARK 500 NE2 HIS X 294 O HOH X 2516 2.19 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 X 2343 O HOH X 2564 3645 2.19 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 X 19 CG ARG X 19 CD -0.161 REMARK 500 GLN X 60 CB GLN X 60 CG -0.196 REMARK 500 MET X 270 SD MET X 270 CE -0.341 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN X 60 CB - CA - C ANGL. DEV. = -14.6 DEGREES REMARK 500 GLN X 60 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG X 164 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP X 244 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 MET X 270 CG - SD - CE ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG X 290 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG X 290 NE - CZ - NH2 ANGL. DEV. = -4.9 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 ALA X 2 -101.15 -41.17 REMARK 500 GLU X 3 121.53 84.02 REMARK 500 GLU X 57 150.60 -49.01 REMARK 500 LEU X 74 43.66 -140.42 REMARK 500 TRP X 225 -106.19 -111.99 REMARK 500 ASP X 331 38.93 -99.93 REMARK 500 TYR X 358 -64.31 -130.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA X 2 GLU X 3 142.74 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 X2006 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH X2008 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH X2011 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH X2018 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH X2027 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH X2032 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH X2171 DISTANCE = 5.92 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "XB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN X 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TNF X 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GVO RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED REMARK 900 WITH 2,4 DINITROPHENOL REMARK 900 RELATED ID: 1GVQ RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED REMARK 900 WITH 2-CYCLOHEXENONE REMARK 900 RELATED ID: 1GVR RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED REMARK 900 WITH 2,4 DINITROPHENOL REMARK 900 RELATED ID: 1GVS RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED REMARK 900 WITH 2,4 DINITROPHENOL REMARK 900 RELATED ID: 1H50 RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXES REMARK 900 RELATED ID: 1H51 RELATED DB: PDB REMARK 900 OXIDISED PENTAERYTHRITOL TETRANITRATE REDUCTASE (SCN COMPLEX) REMARK 900 RELATED ID: 1H60 RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH REMARK 900 PROGESTERONE REMARK 900 RELATED ID: 1H61 RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH REMARK 900 PREDNISONE REMARK 900 RELATED ID: 1H62 RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH REMARK 900 1,4-ANDROSTADIEN- 3,17-DIONE REMARK 900 RELATED ID: 1H63 RELATED DB: PDB REMARK 900 STRUCTURE OF THE REDUCED PENTAERYTHRITOL TETRANITRATE REDUCTASE REMARK 900 RELATED ID: 1VYP RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE F102Y MUTANT REMARK 900 AND COMPLEXED WITH PICRIC ACID REMARK 900 RELATED ID: 1VYR RELATED DB: PDB REMARK 900 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE COMPLEXED WITH REMARK 900 PICRIC ACID DBREF 1VYS X 1 364 UNP P71278 P71278_ENTCL 2 365 SEQADV 1VYS TYR X 102 UNP P71278 TRP 103 ENGINEERED MUTATION SEQRES 1 X 364 SER ALA GLU LYS LEU PHE THR PRO LEU LYS VAL GLY ALA SEQRES 2 X 364 VAL THR ALA PRO ASN ARG VAL PHE MET ALA PRO LEU THR SEQRES 3 X 364 ARG LEU ARG SER ILE GLU PRO GLY ASP ILE PRO THR PRO SEQRES 4 X 364 LEU MET GLY GLU TYR TYR ARG GLN ARG ALA SER ALA GLY SEQRES 5 X 364 LEU ILE ILE SER GLU ALA THR GLN ILE SER ALA GLN ALA SEQRES 6 X 364 LYS GLY TYR ALA GLY ALA PRO GLY LEU HIS SER PRO GLU SEQRES 7 X 364 GLN ILE ALA ALA TRP LYS LYS ILE THR ALA GLY VAL HIS SEQRES 8 X 364 ALA GLU ASP GLY ARG ILE ALA VAL GLN LEU TYR HIS THR SEQRES 9 X 364 GLY ARG ILE SER HIS SER SER ILE GLN PRO GLY GLY GLN SEQRES 10 X 364 ALA PRO VAL SER ALA SER ALA LEU ASN ALA ASN THR ARG SEQRES 11 X 364 THR SER LEU ARG ASP GLU ASN GLY ASN ALA ILE ARG VAL SEQRES 12 X 364 ASP THR THR THR PRO ARG ALA LEU GLU LEU ASP GLU ILE SEQRES 13 X 364 PRO GLY ILE VAL ASN ASP PHE ARG GLN ALA VAL ALA ASN SEQRES 14 X 364 ALA ARG GLU ALA GLY PHE ASP LEU VAL GLU LEU HIS SER SEQRES 15 X 364 ALA HIS GLY TYR LEU LEU HIS GLN PHE LEU SER PRO SER SEQRES 16 X 364 SER ASN GLN ARG THR ASP GLN TYR GLY GLY SER VAL GLU SEQRES 17 X 364 ASN ARG ALA ARG LEU VAL LEU GLU VAL VAL ASP ALA VAL SEQRES 18 X 364 CYS ASN GLU TRP SER ALA ASP ARG ILE GLY ILE ARG VAL SEQRES 19 X 364 SER PRO ILE GLY THR PHE GLN ASN VAL ASP ASN GLY PRO SEQRES 20 X 364 ASN GLU GLU ALA ASP ALA LEU TYR LEU ILE GLU GLU LEU SEQRES 21 X 364 ALA LYS ARG GLY ILE ALA TYR LEU HIS MET SER GLU THR SEQRES 22 X 364 ASP LEU ALA GLY GLY LYS PRO TYR SER GLU ALA PHE ARG SEQRES 23 X 364 GLN LYS VAL ARG GLU ARG PHE HIS GLY VAL ILE ILE GLY SEQRES 24 X 364 ALA GLY ALA TYR THR ALA GLU LYS ALA GLU ASP LEU ILE SEQRES 25 X 364 GLY LYS GLY LEU ILE ASP ALA VAL ALA PHE GLY ARG ASP SEQRES 26 X 364 TYR ILE ALA ASN PRO ASP LEU VAL ALA ARG LEU GLN LYS SEQRES 27 X 364 LYS ALA GLU LEU ASN PRO GLN ARG PRO GLU SER PHE TYR SEQRES 28 X 364 GLY GLY GLY ALA GLU GLY TYR THR ASP TYR PRO SER LEU HET FMN X 401 31 HET TNF X 500 16 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM TNF PICRIC ACID HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN TNF 2,4,6-TRINITROPHENOL FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 TNF C6 H3 N3 O7 FORMUL 4 HOH *604(H2 O) HELIX 1 1 THR X 38 ARG X 48 1 11 HELIX 2 2 SER X 76 GLU X 93 1 18 HELIX 3 3 HIS X 109 GLN X 113 5 5 HELIX 4 4 GLN X 113 GLN X 117 5 5 HELIX 5 5 GLU X 152 ASP X 154 5 3 HELIX 6 6 GLU X 155 ALA X 173 1 19 HELIX 7 7 TYR X 186 SER X 193 1 8 HELIX 8 8 SER X 206 ALA X 211 1 6 HELIX 9 9 ALA X 211 TRP X 225 1 15 HELIX 10 10 SER X 226 ASP X 228 5 3 HELIX 11 11 ASN X 248 ARG X 263 1 16 HELIX 12 12 SER X 282 PHE X 293 1 12 HELIX 13 13 THR X 304 LYS X 314 1 11 HELIX 14 14 GLY X 323 ASN X 329 1 7 HELIX 15 15 ASP X 331 LYS X 339 1 9 HELIX 16 16 ARG X 346 PHE X 350 5 5 SHEET 1 XA 2 LEU X 9 VAL X 11 0 SHEET 2 XA 2 VAL X 14 ALA X 16 -1 O VAL X 14 N VAL X 11 SHEET 1 XB 9 VAL X 20 MET X 22 0 SHEET 2 XB 9 ALA X 319 PHE X 322 1 O VAL X 320 N PHE X 21 SHEET 3 XB 9 VAL X 296 ALA X 300 1 O GLY X 299 N ALA X 321 SHEET 4 XB 9 TYR X 267 SER X 271 1 O LEU X 268 N ILE X 298 SHEET 5 XB 9 ILE X 230 VAL X 234 1 O ILE X 232 N HIS X 269 SHEET 6 XB 9 LEU X 177 SER X 182 1 O VAL X 178 N GLY X 231 SHEET 7 XB 9 ILE X 97 TYR X 102 1 O VAL X 99 N GLU X 179 SHEET 8 XB 9 LEU X 53 GLN X 60 1 O ILE X 54 N ALA X 98 SHEET 9 XB 9 VAL X 20 MET X 22 1 O MET X 22 N ILE X 55 SHEET 1 XC 2 VAL X 120 SER X 121 0 SHEET 2 XC 2 ARG X 149 ALA X 150 1 O ARG X 149 N SER X 121 SHEET 1 XD 2 ARG X 130 ARG X 134 0 SHEET 2 XD 2 ALA X 140 ASP X 144 -1 O ILE X 141 N LEU X 133 CISPEP 1 GLU X 32 PRO X 33 0 1.39 SITE 1 AC1 20 ALA X 23 PRO X 24 LEU X 25 THR X 26 SITE 2 AC1 20 ALA X 58 GLN X 100 HIS X 181 HIS X 184 SITE 3 AC1 20 ARG X 233 LEU X 275 ALA X 302 GLY X 323 SITE 4 AC1 20 ARG X 324 TYR X 351 TNF X 500 HOH X2518 SITE 5 AC1 20 HOH X2601 HOH X2602 HOH X2603 HOH X2604 SITE 1 AC2 11 THR X 26 ALA X 58 TYR X 68 TYR X 102 SITE 2 AC2 11 HIS X 181 HIS X 184 TYR X 186 GLN X 241 SITE 3 AC2 11 TYR X 351 FMN X 401 HOH X2575 CRYST1 56.591 68.330 88.603 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 0.017671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011286 0.00000