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 6 30-OCT-24 3KWK 1 REMARK 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 CONECT 250 251 CONECT 251 250 252 254 CONECT 252 251 253 258 CONECT 253 252 CONECT 254 251 255 CONECT 255 254 256 CONECT 256 255 257 CONECT 257 256 CONECT 258 252 CONECT 297 299 CONECT 298 300 CONECT 299 297 301 305 CONECT 300 298 302 306 CONECT 301 299 303 313 CONECT 302 300 304 313 CONECT 303 301 CONECT 304 302 CONECT 305 299 307 CONECT 306 300 308 CONECT 307 305 309 CONECT 308 306 310 CONECT 309 307 311 CONECT 310 308 312 CONECT 311 309 CONECT 312 310 CONECT 313 301 302 CONECT 514 515 CONECT 515 514 516 518 CONECT 516 515 517 522 CONECT 517 516 CONECT 518 515 519 CONECT 519 518 520 CONECT 520 519 521 CONECT 521 520 CONECT 522 516 CONECT 578 579 CONECT 579 578 580 582 CONECT 580 579 581 586 CONECT 581 580 CONECT 582 579 583 CONECT 583 582 584 CONECT 584 583 585 CONECT 585 584 CONECT 586 580 CONECT 877 878 CONECT 878 877 879 881 CONECT 879 878 880 885 CONECT 880 879 CONECT 881 878 882 CONECT 882 881 883 CONECT 883 882 884 CONECT 884 883 CONECT 885 879 CONECT 1003 1004 CONECT 1004 1003 1005 1007 CONECT 1005 1004 1006 1011 CONECT 1006 1005 CONECT 1007 1004 1008 CONECT 1008 1007 1009 CONECT 1009 1008 1010 CONECT 1010 1009 CONECT 1011 1005 CONECT 1434 1435 1451 CONECT 1435 1434 1436 1437 CONECT 1436 1435 CONECT 1437 1435 1438 CONECT 1438 1437 1439 1440 CONECT 1439 1438 CONECT 1440 1438 1441 1451 CONECT 1441 1440 1442 CONECT 1442 1441 1443 1449 CONECT 1443 1442 1444 CONECT 1444 1443 1445 1446 CONECT 1445 1444 CONECT 1446 1444 1447 1448 CONECT 1447 1446 CONECT 1448 1446 1449 CONECT 1449 1442 1448 1450 CONECT 1450 1449 1451 1452 CONECT 1451 1434 1440 1450 CONECT 1452 1450 1453 CONECT 1453 1452 1454 1455 CONECT 1454 1453 CONECT 1455 1453 1456 1457 CONECT 1456 1455 CONECT 1457 1455 1458 1459 CONECT 1458 1457 CONECT 1459 1457 1460 CONECT 1460 1459 1461 CONECT 1461 1460 1462 1463 1464 CONECT 1462 1461 CONECT 1463 1461 CONECT 1464 1461 MASTER 370 0 9 8 8 0 7 6 1636 1 93 14 END