HEADER OXIDOREDUCTASE 01-DEC-09 3KWK TITLE CRYSTAL STRUCTURE OF PUTATIVE NADH DEHYDROGENASE/NAD(P)H TITLE 2 NITROREDUCTASE (NP_809094.1) FROM BACTEROIDES THETAIOTAOMICRON VPI- TITLE 3 5482 AT 1.54 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NADH DEHYDROGENASE/NAD(P)H NITROREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 GENE: BT_0181; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PUTATIVE NADH DEHYDROGENASE/NAD(P)H NITROREDUCTASE, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-2, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3KWK 1 REMARK SEQADV REVDAT 4 17-JUL-19 3KWK 1 REMARK LINK REVDAT 3 25-OCT-17 3KWK 1 REMARK REVDAT 2 13-JUL-11 3KWK 1 VERSN REVDAT 1 15-DEC-09 3KWK 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE NADH DEHYDROGENASE/NAD(P)H JRNL TITL 2 NITROREDUCTASE (NP_809094.1) FROM BACTEROIDES JRNL TITL 3 THETAIOTAOMICRON VPI-5482 AT 1.54 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 25811 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1313 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1333 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.07000 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): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 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): 1505 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1044 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2051 ; 1.564 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2547 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 187 ; 5.713 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;34.200 ;23.538 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 268 ;12.520 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.801 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 213 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1691 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 305 ; 0.002 ; 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): 905 ; 1.454 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 356 ; 0.439 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1465 ; 2.379 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 600 ; 4.223 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 586 ; 6.297 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 32 A 199 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4788 9.9865 85.5659 REMARK 3 T TENSOR REMARK 3 T11: 0.0111 T22: 0.0039 REMARK 3 T33: 0.0110 T12: 0.0017 REMARK 3 T13: -0.0017 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.3309 L22: 0.3594 REMARK 3 L33: 0.5437 L12: -0.0251 REMARK 3 L13: -0.1206 L23: 0.0977 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: 0.0258 S13: -0.0010 REMARK 3 S21: -0.0223 S22: 0.0117 S23: -0.0348 REMARK 3 S31: 0.0275 S32: -0.0125 S33: -0.0128 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. REMARK 3 4. AN UNKNOWN LIGAND (UNL) WAS MODELED IN THE PUTATIVE ACTIVE REMARK 3 SITE. CHLORIDE MODELED IS PRESENT IN CRYSTALLIZATION CONDITIONS. REMARK 4 REMARK 4 3KWK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97938 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT MIRROR, VERTICAL AND REMARK 200 HORIZONTAL FOCUSSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25905 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 29.854 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : 0.55000 REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M NAOAC, 30.0000% PEG-4000, 0.1M REMARK 280 TRIS PH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.35650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.10750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.10750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.03475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.10750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.10750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.67825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.10750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.10750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.03475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.10750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.10750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.67825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.35650 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 300 REMARK: SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING REMARK 300 SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT REMARK 300 OLIGOMERIZATION STATE IN SOLUTION. 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: 9080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 186.71300 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 GLY A 0 REMARK 465 GLU A 26 REMARK 465 LYS A 27 REMARK 465 GLY A 28 REMARK 465 THR A 29 REMARK 465 THR A 30 REMARK 465 GLY A 31 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 NZ LYS A 193 O HOH A 259 2.19 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 47 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.8 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 LYS A 73 19.87 55.86 REMARK 500 LYS A 73 18.98 57.83 REMARK 500 ALA A 148 -84.15 -103.53 REMARK 500 ASN A 197 -40.83 71.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396185 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE: THE CONSTRUCT (RESIDUES 26-199) WAS EXPRESSED WITH A REMARK 999 PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3KWK A 26 199 UNP Q8ABC9 Q8ABC9_BACTN 26 199 SEQADV 3KWK GLY A 0 UNP Q8ABC9 EXPRESSION TAG SEQRES 1 A 175 GLY GLU LYS GLY THR THR GLY THR GLY ASN ALA ALA LEU SEQRES 2 A 175 ASP ASN ILE PHE GLU ARG LYS SER VAL ARG THR TYR LEU SEQRES 3 A 175 ASN LYS GLY VAL GLU LYS GLU LYS ILE ASP LEU MSE LEU SEQRES 4 A 175 ARG ALA GLY MSE SER ALA PRO SER GLY LYS ASP VAL ARG SEQRES 5 A 175 PRO TRP GLU PHE VAL VAL VAL SER ASP ARG ALA LYS LEU SEQRES 6 A 175 ASP SER MSE ALA ALA ALA LEU PRO TYR ALA LYS MSE LEU SEQRES 7 A 175 THR GLN ALA ARG ASN ALA ILE ILE VAL CYS GLY ASP SER SEQRES 8 A 175 ALA ARG SER PHE TYR TRP TYR LEU ASP CYS SER ALA ALA SEQRES 9 A 175 ALA GLN ASN ILE LEU LEU ALA ALA GLU SER MSE GLY LEU SEQRES 10 A 175 GLY ALA VAL TRP THR ALA ALA TYR PRO TYR GLU ASP ARG SEQRES 11 A 175 MSE GLU VAL VAL ARG LYS TYR THR HIS LEU PRO GLU ASN SEQRES 12 A 175 ILE LEU PRO LEU CYS VAL ILE PRO PHE GLY TYR PRO ALA SEQRES 13 A 175 THR LYS GLU GLN PRO LYS GLN LYS TYR ASP GLU LYS LYS SEQRES 14 A 175 ILE HIS TYR ASN GLN TYR MODRES 3KWK MSE A 62 MET SELENOMETHIONINE MODRES 3KWK MSE A 67 MET SELENOMETHIONINE MODRES 3KWK MSE A 92 MET SELENOMETHIONINE MODRES 3KWK MSE A 101 MET SELENOMETHIONINE MODRES 3KWK MSE A 139 MET SELENOMETHIONINE MODRES 3KWK MSE A 155 MET SELENOMETHIONINE HET MSE A 62 8 HET MSE A 67 16 HET MSE A 92 8 HET MSE A 101 8 HET MSE A 139 8 HET MSE A 155 8 HET FMN A 300 31 HET UNL A 1 2 HET CL A 2 1 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM UNL UNKNOWN LIGAND HETNAM CL CHLORIDE ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 4 CL CL 1- FORMUL 5 HOH *269(H2 O) HELIX 1 1 ASN A 34 ARG A 43 1 10 HELIX 2 2 GLU A 55 MSE A 67 1 13 HELIX 3 3 SER A 71 VAL A 75 5 5 HELIX 4 4 ASP A 85 LEU A 96 1 12 HELIX 5 5 ALA A 99 ALA A 105 5 7 HELIX 6 6 TYR A 120 MSE A 139 1 20 HELIX 7 7 TYR A 151 HIS A 163 1 13 HELIX 8 8 ASP A 190 ILE A 194 5 5 SHEET 1 A 4 TRP A 78 VAL A 83 0 SHEET 2 A 4 ASN A 107 ASP A 114 -1 O ALA A 108 N VAL A 83 SHEET 3 A 4 ILE A 168 GLY A 177 -1 O LEU A 171 N VAL A 111 SHEET 4 A 4 GLY A 142 ALA A 143 -1 N GLY A 142 O GLY A 177 SHEET 1 B 4 TRP A 78 VAL A 83 0 SHEET 2 B 4 ASN A 107 ASP A 114 -1 O ALA A 108 N VAL A 83 SHEET 3 B 4 ILE A 168 GLY A 177 -1 O LEU A 171 N VAL A 111 SHEET 4 B 4 THR A 146 ALA A 147 -1 N THR A 146 O VAL A 173 LINK C MSE A 62 N LEU A 63 1555 1555 1.33 LINK C AMSE A 67 N SER A 68 1555 1555 1.33 LINK C BMSE A 67 N SER A 68 1555 1555 1.34 LINK C MSE A 92 N ALA A 93 1555 1555 1.33 LINK C MSE A 101 N LEU A 102 1555 1555 1.33 LINK C MSE A 139 N GLY A 140 1555 1555 1.33 LINK C MSE A 155 N GLU A 156 1555 1555 1.33 CISPEP 1 TYR A 149 PRO A 150 0 6.39 SITE 1 AC1 22 HOH A 7 ARG A 43 LYS A 44 SER A 45 SITE 2 AC1 22 ARG A 47 PRO A 70 SER A 71 GLY A 72 SITE 3 AC1 22 ASP A 74 TYR A 98 MSE A 101 ASP A 124 SITE 4 AC1 22 VAL A 144 TRP A 145 THR A 146 ALA A 147 SITE 5 AC1 22 ARG A 154 LYS A 186 LYS A 188 HOH A 275 SITE 6 AC1 22 HOH A 293 HOH A 296 SITE 1 AC2 4 GLN A 187 LYS A 188 TYR A 189 HOH A 257 CRYST1 42.215 42.215 186.713 90.00 90.00 90.00 P 43 21 2 8 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 0.023688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005356 0.00000