HEADER FLAVOPROTEIN 18-SEP-08 3EK3 TITLE CRYSTAL STRUCTURE OF NITROREDUCTASE WITH BOUND FMN (YP_211706.1) FROM TITLE 2 BACTEROIDES FRAGILIS NCTC 9343 AT 1.70 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS NCTC 9343; SOURCE 3 ORGANISM_TAXID: 272559; SOURCE 4 GENE: YP_211706.1, BF2078; 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 YP_211706.1, NITROREDUCTASE WITH BOUND FMN, STRUCTURAL GENOMICS, KEYWDS 2 JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, PSI, OXIDOREDUCTASE, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3EK3 1 REMARK SEQADV REVDAT 5 24-JUL-19 3EK3 1 REMARK LINK REVDAT 4 25-OCT-17 3EK3 1 REMARK REVDAT 3 13-JUL-11 3EK3 1 VERSN REVDAT 2 24-FEB-09 3EK3 1 VERSN REVDAT 1 14-OCT-08 3EK3 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF NITROREDUCTASE WITH BOUND FMN JRNL TITL 2 (YP_211706.1) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.70 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 21941 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) : 0.150 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1124 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1521 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1437 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.39000 REMARK 3 B22 (A**2) : 2.35000 REMARK 3 B33 (A**2) : -0.95000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.552 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1572 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1017 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2156 ; 1.367 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2496 ; 0.926 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 200 ; 5.394 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 66 ;37.756 ;24.697 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 253 ;12.202 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.226 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 242 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1726 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 296 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 309 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1081 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 767 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 776 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 165 ; 0.252 ; 0.200 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): 21 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 47 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.139 ; 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): 1016 ; 1.803 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 386 ; 0.477 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 2.204 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 734 ; 3.881 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 615 ; 5.061 ;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 3 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5379 27.6876 17.5388 REMARK 3 T TENSOR REMARK 3 T11: 0.0405 T22: 0.0147 REMARK 3 T33: 0.0589 T12: -0.0051 REMARK 3 T13: 0.0001 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 0.5338 L22: 0.3766 REMARK 3 L33: 1.1260 L12: -0.0547 REMARK 3 L13: -0.0263 L23: 0.0972 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: 0.0987 S13: 0.0255 REMARK 3 S21: -0.0378 S22: 0.0044 S23: 0.0429 REMARK 3 S31: 0.0395 S32: -0.0404 S33: -0.0060 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO REMARK 3 PARTIAL S-MET INCORPORATION. 4. 2-METHYL-2,4-PENTANEDIOL MOLECULES REMARK 3 FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. REMARK 3 5. AN UNKOWN LIGAND (UNL) WAS MODELED INTO THE PUTATIVE IN THE REMARK 3 VICINITY OF A BOUND FLAVIN MONONUCLEOTIDE (FMN) COFACTOR. REMARK 4 REMARK 4 3EK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97932,0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21975 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.123 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 47.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65.0000% MPD, 0.1M TRIS PH 8.0, VAPOR REMARK 280 DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K, VAPOR REMARK 280 DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.25500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.25500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.30500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.86500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.30500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.86500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.25500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.30500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.86500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.25500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.30500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.86500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.25500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 394 LIES ON A SPECIAL POSITION. 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 MSE A 1 REMARK 465 LYS A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 21 CZ NH1 NH2 REMARK 470 LYS A 22 CD CE NZ REMARK 470 LYS A 76 NZ REMARK 470 HIS A 77 ND1 CD2 CE1 NE2 REMARK 470 ARG A 79 CZ NH1 NH2 REMARK 470 LYS A 169 NZ REMARK 470 LYS A 176 CD CE NZ 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391613 RELATED DB: TARGETDB DBREF 3EK3 A 1 189 UNP Q5LDN3 Q5LDN3_BACFN 1 189 SEQADV 3EK3 GLY A 0 UNP Q5LDN3 EXPRESSION TAG SEQRES 1 A 190 GLY MSE LYS THR ASN GLU VAL LEU GLU THR ILE LYS ALA SEQRES 2 A 190 ARG ARG SER VAL ARG ALA TYR ASP ARG LYS GLN ILE PRO SEQRES 3 A 190 ALA ASP ASP LEU ASN ALA ILE LEU GLU ALA GLY ALA TYR SEQRES 4 A 190 ALA PRO SER GLY MSE HIS TYR GLU THR TRP HIS PHE THR SEQRES 5 A 190 ALA VAL CYS ASN THR VAL LYS LEU GLU GLU LEU ASN GLU SEQRES 6 A 190 ARG ILE LYS GLY ALA PHE ALA LYS SER ASP ASP LYS HIS SEQRES 7 A 190 LEU ARG GLU ARG GLY HIS SER GLU THR TYR CYS CYS TYR SEQRES 8 A 190 TYR HIS ALA PRO THR LEU VAL ILE VAL SER ASN GLU PRO SEQRES 9 A 190 LYS GLN TRP TRP ALA GLY MSE ASP CYS ALA CYS ALA ILE SEQRES 10 A 190 GLU ASN MSE PHE LEU ALA ALA THR SER LEU GLY ILE ALA SEQRES 11 A 190 SER CYS TRP ILE ASN GLN LEU GLY THR THR CYS ASP ASP SEQRES 12 A 190 PRO GLU VAL ARG ALA TYR LEU THR SER LEU GLY VAL PRO SEQRES 13 A 190 GLU ASN HIS LYS VAL TYR GLY CYS VAL ALA LEU GLY TYR SEQRES 14 A 190 LYS ALA GLU GLY ALA LEU LEU LYS GLU LYS THR VAL LYS SEQRES 15 A 190 ALA GLY THR ILE THR ILE VAL GLU MODRES 3EK3 MSE A 43 MET SELENOMETHIONINE MODRES 3EK3 MSE A 110 MET SELENOMETHIONINE MODRES 3EK3 MSE A 119 MET SELENOMETHIONINE HET MSE A 43 8 HET MSE A 110 8 HET MSE A 119 8 HET FMN A 200 31 HET UNL A 201 8 HET MPD A 202 8 HET MPD A 203 16 HET MPD A 204 8 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM UNL UNKNOWN LIGAND HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 4 MPD 3(C6 H14 O2) FORMUL 7 HOH *205(H2 O) HELIX 1 1 ASN A 4 ARG A 13 1 10 HELIX 2 2 PRO A 25 TYR A 38 1 14 HELIX 3 3 SER A 41 TYR A 45 5 5 HELIX 4 4 ASN A 55 LYS A 72 1 18 HELIX 5 5 ASP A 75 HIS A 83 1 9 HELIX 6 6 TRP A 107 LEU A 126 1 20 HELIX 7 7 ASP A 142 GLY A 153 1 12 SHEET 1 A 4 HIS A 49 VAL A 53 0 SHEET 2 A 4 THR A 95 ASN A 101 -1 O LEU A 96 N VAL A 53 SHEET 3 A 4 LYS A 159 GLY A 167 -1 O VAL A 164 N VAL A 97 SHEET 4 A 4 ALA A 129 ILE A 133 -1 N ILE A 133 O CYS A 163 LINK C GLY A 42 N MSE A 43 1555 1555 1.34 LINK C MSE A 43 N HIS A 44 1555 1555 1.34 LINK C GLY A 109 N MSE A 110 1555 1555 1.34 LINK C MSE A 110 N ASP A 111 1555 1555 1.33 LINK C ASN A 118 N MSE A 119 1555 1555 1.32 LINK C MSE A 119 N PHE A 120 1555 1555 1.34 SITE 1 AC1 20 ARG A 13 ARG A 14 SER A 15 ARG A 17 SITE 2 AC1 20 PRO A 40 SER A 41 GLY A 42 HIS A 44 SITE 3 AC1 20 TYR A 91 CYS A 131 TRP A 132 ASN A 134 SITE 4 AC1 20 GLN A 135 LYS A 178 UNL A 201 MPD A 202 SITE 5 AC1 20 MPD A 204 HOH A 217 HOH A 225 HOH A 265 SITE 1 AC2 7 MSE A 43 TYR A 91 TRP A 107 ASN A 134 SITE 2 AC2 7 FMN A 200 MPD A 204 HOH A 289 SITE 1 AC3 7 ARG A 14 HIS A 44 FMN A 200 HOH A 217 SITE 2 AC3 7 HOH A 261 HOH A 265 HOH A 368 SITE 1 AC4 7 TRP A 106 GLY A 137 THR A 138 LYS A 159 SITE 2 AC4 7 VAL A 160 TYR A 161 HOH A 401 SITE 1 AC5 4 ARG A 17 MSE A 43 FMN A 200 UNL A 201 CRYST1 40.610 83.730 116.510 90.00 90.00 90.00 C 2 2 21 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 0.024624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011943 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008583 0.00000