HEADER OXIDOREDUCTASE 19-NOV-07 3BEM TITLE CRYSTAL STRUCTURE OF PUTATIVE NITROREDUCTASE YDFN (2632848) FROM TITLE 2 BACILLUS SUBTILIS AT 1.65 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NAD(P)H NITROREDUCTASE YDFN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.-.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: 2632848, YDFN, BSU05480; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MH4A KEYWDS 2632848, PUTATIVE NITROREDUCTASE YDFN, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, FLAVOPROTEIN, FMN, NAD, NADP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 25-JAN-23 3BEM 1 SEQADV REVDAT 7 20-OCT-21 3BEM 1 REMARK SEQADV REVDAT 6 24-JUL-19 3BEM 1 REMARK LINK REVDAT 5 25-OCT-17 3BEM 1 REMARK REVDAT 4 13-JUL-11 3BEM 1 VERSN REVDAT 3 24-FEB-09 3BEM 1 VERSN REVDAT 2 11-DEC-07 3BEM 1 SOURCE REVDAT 1 04-DEC-07 3BEM 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE NITROREDUCTASE YDFN (2632848) JRNL TITL 2 FROM BACILLUS SUBTILIS AT 1.65 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 51310 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2620 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3516 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.40000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.982 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3599 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2390 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4890 ; 1.610 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5851 ; 0.997 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 5.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;38.588 ;24.709 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 638 ;13.864 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;14.714 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4083 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 722 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 814 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2623 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1791 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1866 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 279 ; 0.154 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.107 ; 0.200 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): 19 ; 0.327 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.217 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.246 ; 0.200 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): 2271 ; 2.433 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 880 ; 0.570 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3530 ; 3.069 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1584 ; 5.078 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1356 ; 7.211 ;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 : 2 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 0 A 206 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4180 8.8900 44.9240 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: -0.0274 REMARK 3 T33: -0.0300 T12: 0.0113 REMARK 3 T13: 0.0014 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.3311 L22: 0.4366 REMARK 3 L33: 0.7819 L12: 0.1480 REMARK 3 L13: 0.2156 L23: 0.2223 REMARK 3 S TENSOR REMARK 3 S11: -0.0253 S12: 0.0116 S13: 0.0011 REMARK 3 S21: -0.0124 S22: 0.0255 S23: -0.0219 REMARK 3 S31: -0.0424 S32: 0.0689 S33: -0.0002 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -3 B 206 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4100 0.0680 49.8390 REMARK 3 T TENSOR REMARK 3 T11: 0.0219 T22: -0.0134 REMARK 3 T33: -0.0230 T12: 0.0078 REMARK 3 T13: 0.0004 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.3744 L22: 0.5402 REMARK 3 L33: 0.9499 L12: 0.3024 REMARK 3 L13: 0.1294 L23: 0.0171 REMARK 3 S TENSOR REMARK 3 S11: 0.0279 S12: -0.0261 S13: -0.0224 REMARK 3 S21: 0.0293 S22: -0.0131 S23: 0.0251 REMARK 3 S31: 0.0610 S32: -0.0869 S33: -0.0149 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 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. REMARK 3 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 4. ACETATE AND 1,2-PROPANEDIOL WERE MODELED BASED ON REMARK 3 CRYSTALLIZATION REMARK 3 CONDITIONS. REMARK 3 5. NI MODELED BASED ON GEOMETRY AND COORDINATION ENVIRONMENT. REMARK 3 6. FMN MODELED BASED ON DENSITY AND PROPOSED FUNCTION. REMARK 4 REMARK 4 3BEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840, 0.97939, 0.97953 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : ADJUSTABLE FOCUSING MIRRORS IN K REMARK 200 -B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 28.583 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 40.0% 1,2-PROPANEDIOL, 0.1M REMARK 280 ACETATE PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.60000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7000 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MSE A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 MSE B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 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 LYS A 186 CG CD CE NZ REMARK 470 THR A 187 OG1 CG2 REMARK 470 GLU A 188 CG CD OE1 OE2 REMARK 470 SER A 189 OG REMARK 470 ARG A 191 CG CD NE CZ NH1 NH2 REMARK 470 HIS B -3 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B -2 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B -1 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 10 CD OE1 OE2 REMARK 470 LYS B 60 CE NZ REMARK 470 GLN B 63 CG CD OE1 NE2 REMARK 470 GLN B 106 CG CD OE1 NE2 REMARK 470 GLU B 188 CG CD OE1 OE2 REMARK 470 SER B 189 OG REMARK 470 ARG B 191 CG CD NE CZ NH1 NH2 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 133 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 193 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 11 NE - CZ - NH2 ANGL. DEV. = -3.0 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 186 97.51 -62.34 REMARK 500 PHE B 42 18.51 59.19 REMARK 500 ALA B 65 38.88 -91.07 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 HIS B -3 HIS B -2 -141.99 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 400 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 6 NE2 REMARK 620 2 GLU A 10 OE1 95.3 REMARK 620 3 GLU A 10 OE2 93.7 54.0 REMARK 620 4 HOH B 450 O 84.2 162.9 109.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 381891 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHH. THE CONSTRUCT WAS ENGINEERED WITH THE REMARK 999 FOLLOWING MUTATIONS: RESIDUES LYS 147, GLU 148, AND REMARK 999 LYS 149 WERE MUTATED TO ALA. DBREF 3BEM A 1 206 UNP P96692 YDFN_BACSU 1 206 DBREF 3BEM B 1 206 UNP P96692 YDFN_BACSU 1 206 SEQADV 3BEM MSE A -11 UNP P96692 EXPRESSION TAG SEQADV 3BEM GLY A -10 UNP P96692 EXPRESSION TAG SEQADV 3BEM SER A -9 UNP P96692 EXPRESSION TAG SEQADV 3BEM ASP A -8 UNP P96692 EXPRESSION TAG SEQADV 3BEM LYS A -7 UNP P96692 EXPRESSION TAG SEQADV 3BEM ILE A -6 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A -5 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A -4 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A -3 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A -2 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A -1 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS A 0 UNP P96692 EXPRESSION TAG SEQADV 3BEM ALA A 147 UNP P96692 LYS 147 ENGINEERED MUTATION SEQADV 3BEM ALA A 148 UNP P96692 GLU 148 ENGINEERED MUTATION SEQADV 3BEM ALA A 149 UNP P96692 LYS 149 ENGINEERED MUTATION SEQADV 3BEM MSE B -11 UNP P96692 EXPRESSION TAG SEQADV 3BEM GLY B -10 UNP P96692 EXPRESSION TAG SEQADV 3BEM SER B -9 UNP P96692 EXPRESSION TAG SEQADV 3BEM ASP B -8 UNP P96692 EXPRESSION TAG SEQADV 3BEM LYS B -7 UNP P96692 EXPRESSION TAG SEQADV 3BEM ILE B -6 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B -5 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B -4 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B -3 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B -2 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B -1 UNP P96692 EXPRESSION TAG SEQADV 3BEM HIS B 0 UNP P96692 EXPRESSION TAG SEQADV 3BEM ALA B 147 UNP P96692 LYS 147 ENGINEERED MUTATION SEQADV 3BEM ALA B 148 UNP P96692 GLU 148 ENGINEERED MUTATION SEQADV 3BEM ALA B 149 UNP P96692 LYS 149 ENGINEERED MUTATION SEQRES 1 A 218 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 218 ALA GLU PHE THR HIS LEU VAL ASN GLU ARG ARG SER ALA SEQRES 3 A 218 SER ASN PHE LEU SER GLY HIS PRO ILE THR LYS GLU ASP SEQRES 4 A 218 LEU ASN GLU MSE PHE GLU LEU VAL ALA LEU ALA PRO SER SEQRES 5 A 218 ALA PHE ASN LEU GLN HIS THR LYS TYR VAL THR VAL LEU SEQRES 6 A 218 ASP GLN ASP VAL LYS GLU LYS LEU LYS GLN ALA ALA ASN SEQRES 7 A 218 GLY GLN TYR LYS VAL VAL SER SER SER ALA VAL LEU LEU SEQRES 8 A 218 VAL LEU GLY ASP LYS GLN ALA TYR GLN GLN ALA ALA ASP SEQRES 9 A 218 ILE TYR GLU GLY LEU LYS VAL LEU GLY ILE LEU ASN LYS SEQRES 10 A 218 GLN GLU TYR ASP HIS MSE VAL GLN ASP THR VAL SER PHE SEQRES 11 A 218 TYR GLU ASN ARG GLY GLU GLN PHE LYS ARG ASP GLU ALA SEQRES 12 A 218 ILE ARG ASN ALA SER LEU SER ALA MSE MSE PHE MSE LEU SEQRES 13 A 218 SER ALA ALA ALA ALA GLY TRP ASP THR CYS PRO MSE ILE SEQRES 14 A 218 GLY PHE ASP ALA GLU ALA VAL LYS ARG ILE LEU ASN ILE SEQRES 15 A 218 ASP ASP GLN PHE GLU VAL VAL MSE MSE ILE THR ILE GLY SEQRES 16 A 218 LYS GLU LYS THR GLU SER ARG ARG PRO ARG GLY TYR ARG SEQRES 17 A 218 LYS PRO VAL ASN GLU PHE VAL GLU TYR MSE SEQRES 1 B 218 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 B 218 ALA GLU PHE THR HIS LEU VAL ASN GLU ARG ARG SER ALA SEQRES 3 B 218 SER ASN PHE LEU SER GLY HIS PRO ILE THR LYS GLU ASP SEQRES 4 B 218 LEU ASN GLU MSE PHE GLU LEU VAL ALA LEU ALA PRO SER SEQRES 5 B 218 ALA PHE ASN LEU GLN HIS THR LYS TYR VAL THR VAL LEU SEQRES 6 B 218 ASP GLN ASP VAL LYS GLU LYS LEU LYS GLN ALA ALA ASN SEQRES 7 B 218 GLY GLN TYR LYS VAL VAL SER SER SER ALA VAL LEU LEU SEQRES 8 B 218 VAL LEU GLY ASP LYS GLN ALA TYR GLN GLN ALA ALA ASP SEQRES 9 B 218 ILE TYR GLU GLY LEU LYS VAL LEU GLY ILE LEU ASN LYS SEQRES 10 B 218 GLN GLU TYR ASP HIS MSE VAL GLN ASP THR VAL SER PHE SEQRES 11 B 218 TYR GLU ASN ARG GLY GLU GLN PHE LYS ARG ASP GLU ALA SEQRES 12 B 218 ILE ARG ASN ALA SER LEU SER ALA MSE MSE PHE MSE LEU SEQRES 13 B 218 SER ALA ALA ALA ALA GLY TRP ASP THR CYS PRO MSE ILE SEQRES 14 B 218 GLY PHE ASP ALA GLU ALA VAL LYS ARG ILE LEU ASN ILE SEQRES 15 B 218 ASP ASP GLN PHE GLU VAL VAL MSE MSE ILE THR ILE GLY SEQRES 16 B 218 LYS GLU LYS THR GLU SER ARG ARG PRO ARG GLY TYR ARG SEQRES 17 B 218 LYS PRO VAL ASN GLU PHE VAL GLU TYR MSE MODRES 3BEM MSE A 1 MET SELENOMETHIONINE MODRES 3BEM MSE A 31 MET SELENOMETHIONINE MODRES 3BEM MSE A 111 MET SELENOMETHIONINE MODRES 3BEM MSE A 140 MET SELENOMETHIONINE MODRES 3BEM MSE A 141 MET SELENOMETHIONINE MODRES 3BEM MSE A 143 MET SELENOMETHIONINE MODRES 3BEM MSE A 156 MET SELENOMETHIONINE MODRES 3BEM MSE A 178 MET SELENOMETHIONINE MODRES 3BEM MSE A 179 MET SELENOMETHIONINE MODRES 3BEM MSE A 206 MET SELENOMETHIONINE MODRES 3BEM MSE B 1 MET SELENOMETHIONINE MODRES 3BEM MSE B 31 MET SELENOMETHIONINE MODRES 3BEM MSE B 111 MET SELENOMETHIONINE MODRES 3BEM MSE B 140 MET SELENOMETHIONINE MODRES 3BEM MSE B 141 MET SELENOMETHIONINE MODRES 3BEM MSE B 143 MET SELENOMETHIONINE MODRES 3BEM MSE B 156 MET SELENOMETHIONINE MODRES 3BEM MSE B 178 MET SELENOMETHIONINE MODRES 3BEM MSE B 179 MET SELENOMETHIONINE MODRES 3BEM MSE B 206 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 31 8 HET MSE A 111 8 HET MSE A 140 8 HET MSE A 141 16 HET MSE A 143 8 HET MSE A 156 16 HET MSE A 178 16 HET MSE A 179 8 HET MSE A 206 9 HET MSE B 1 8 HET MSE B 31 8 HET MSE B 111 8 HET MSE B 140 8 HET MSE B 141 13 HET MSE B 143 8 HET MSE B 156 8 HET MSE B 178 8 HET MSE B 179 13 HET MSE B 206 14 HET NI A 400 1 HET ACT A 401 4 HET FMN A 300 31 HET PGO A 402 5 HET FMN B 300 31 HET PGO B 301 5 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION HETNAM ACT ACETATE ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM PGO S-1,2-PROPANEDIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 3 NI NI 2+ FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 FMN 2(C17 H21 N4 O9 P) FORMUL 6 PGO 2(C3 H8 O2) FORMUL 9 HOH *335(H2 O) HELIX 1 1 HIS A 0 ARG A 11 1 12 HELIX 2 2 THR A 24 ALA A 36 1 13 HELIX 3 3 SER A 40 LEU A 44 5 5 HELIX 4 4 ASP A 54 ALA A 64 1 11 HELIX 5 5 TYR A 69 SER A 74 1 6 HELIX 6 6 GLN A 85 GLN A 88 5 4 HELIX 7 7 GLN A 89 LEU A 100 1 12 HELIX 8 8 ASN A 104 GLY A 123 1 20 HELIX 9 9 GLY A 123 ALA A 149 1 27 HELIX 10 10 ASP A 160 ASN A 169 1 10 HELIX 11 11 LYS A 186 ARG A 190 5 5 HELIX 12 12 PRO A 198 GLU A 201 5 4 HELIX 13 13 HIS B -1 ARG B 11 1 13 HELIX 14 14 THR B 24 ALA B 36 1 13 HELIX 15 15 SER B 40 LEU B 44 5 5 HELIX 16 16 ASP B 54 ALA B 65 1 12 HELIX 17 17 TYR B 69 SER B 74 1 6 HELIX 18 18 GLN B 85 GLN B 88 5 4 HELIX 19 19 GLN B 89 LEU B 100 1 12 HELIX 20 20 ASN B 104 GLY B 123 1 20 HELIX 21 21 GLY B 123 GLY B 150 1 28 HELIX 22 22 ASP B 160 ASN B 169 1 10 HELIX 23 23 LYS B 186 ARG B 190 5 5 HELIX 24 24 PRO B 198 GLU B 201 5 4 SHEET 1 A 5 ASP A 152 MSE A 156 0 SHEET 2 A 5 PHE A 174 GLY A 183 -1 O MSE A 179 N MSE A 156 SHEET 3 A 5 ALA A 76 ASP A 83 -1 N LEU A 78 O ILE A 180 SHEET 4 A 5 THR A 47 VAL A 52 -1 N VAL A 52 O VAL A 77 SHEET 5 A 5 VAL B 203 MSE B 206 1 O GLU B 204 N THR A 51 SHEET 1 B 5 VAL A 203 MSE A 206 0 SHEET 2 B 5 THR B 47 VAL B 52 1 O THR B 51 N GLU A 204 SHEET 3 B 5 ALA B 76 ASP B 83 -1 O LEU B 81 N LYS B 48 SHEET 4 B 5 PHE B 174 GLY B 183 -1 O MSE B 178 N VAL B 80 SHEET 5 B 5 ASP B 152 MSE B 156 -1 N ASP B 152 O GLY B 183 LINK C HIS A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C GLU A 30 N MSE A 31 1555 1555 1.32 LINK C MSE A 31 N PHE A 32 1555 1555 1.32 LINK C HIS A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N VAL A 112 1555 1555 1.32 LINK C ALA A 139 N MSE A 140 1555 1555 1.33 LINK C MSE A 140 N AMSE A 141 1555 1555 1.32 LINK C MSE A 140 N BMSE A 141 1555 1555 1.33 LINK C AMSE A 141 N PHE A 142 1555 1555 1.33 LINK C BMSE A 141 N PHE A 142 1555 1555 1.33 LINK C PHE A 142 N MSE A 143 1555 1555 1.33 LINK C MSE A 143 N LEU A 144 1555 1555 1.34 LINK C PRO A 155 N AMSE A 156 1555 1555 1.33 LINK C PRO A 155 N BMSE A 156 1555 1555 1.34 LINK C AMSE A 156 N ILE A 157 1555 1555 1.33 LINK C BMSE A 156 N ILE A 157 1555 1555 1.33 LINK C VAL A 177 N AMSE A 178 1555 1555 1.32 LINK C VAL A 177 N BMSE A 178 1555 1555 1.31 LINK C AMSE A 178 N MSE A 179 1555 1555 1.32 LINK C BMSE A 178 N MSE A 179 1555 1555 1.32 LINK C MSE A 179 N ILE A 180 1555 1555 1.33 LINK C TYR A 205 N MSE A 206 1555 1555 1.33 LINK C HIS B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N ALA B 2 1555 1555 1.32 LINK C GLU B 30 N MSE B 31 1555 1555 1.33 LINK C MSE B 31 N PHE B 32 1555 1555 1.34 LINK C HIS B 110 N MSE B 111 1555 1555 1.33 LINK C MSE B 111 N VAL B 112 1555 1555 1.32 LINK C ALA B 139 N MSE B 140 1555 1555 1.34 LINK C MSE B 140 N MSE B 141 1555 1555 1.34 LINK C MSE B 141 N PHE B 142 1555 1555 1.33 LINK C PHE B 142 N MSE B 143 1555 1555 1.32 LINK C MSE B 143 N LEU B 144 1555 1555 1.35 LINK C PRO B 155 N MSE B 156 1555 1555 1.32 LINK C MSE B 156 N ILE B 157 1555 1555 1.32 LINK C VAL B 177 N MSE B 178 1555 1555 1.32 LINK C MSE B 178 N MSE B 179 1555 1555 1.32 LINK C MSE B 179 N ILE B 180 1555 1555 1.33 LINK C TYR B 205 N AMSE B 206 1555 1555 1.33 LINK C TYR B 205 N BMSE B 206 1555 1555 1.33 LINK NE2 HIS A 6 NI NI A 400 1555 1555 2.10 LINK OE1AGLU A 10 NI NI A 400 1555 1555 2.41 LINK OE2AGLU A 10 NI NI A 400 1555 1555 2.49 LINK NI NI A 400 O HOH B 450 1555 1555 2.23 SITE 1 AC1 4 HIS A 6 GLU A 10 HIS B 0 HOH B 450 SITE 1 AC2 2 TYR A 94 FMN B 300 SITE 1 AC3 19 ARG A 11 ARG A 12 SER A 13 GLN A 68 SITE 2 AC3 19 LYS A 70 CYS A 154 PRO A 155 MSE A 156 SITE 3 AC3 19 ILE A 157 GLY A 158 ARG A 193 ARG A 196 SITE 4 AC3 19 HOH A 468 HOH A 472 PRO B 39 SER B 40 SITE 5 AC3 19 ALA B 41 ASN B 43 LEU B 137 SITE 1 AC4 21 PRO A 39 SER A 40 ALA A 41 ASN A 43 SITE 2 AC4 21 ASN A 134 LEU A 137 ACT A 401 HOH A 488 SITE 3 AC4 21 ARG B 11 ARG B 12 SER B 13 GLN B 68 SITE 4 AC4 21 LYS B 70 CYS B 154 PRO B 155 MSE B 156 SITE 5 AC4 21 ILE B 157 GLY B 158 ARG B 193 ARG B 196 SITE 6 AC4 21 HOH B 335 SITE 1 AC5 4 PRO B 22 ILE B 23 LEU B 53 SER B 75 SITE 1 AC6 6 LEU A 18 SER A 19 GLY A 20 HIS A 21 SITE 2 AC6 6 SER A 73 SER A 75 CRYST1 51.620 69.200 61.850 90.00 100.54 90.00 P 1 21 1 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 0.019372 0.000000 0.003606 0.00000 SCALE2 0.000000 0.014451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016446 0.00000