HEADER OXIDOREDUCTASE 26-FEB-09 3GFA TITLE CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN TITLE 2 (CD3205) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.35 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE NITROREDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM DIFFICILE 630; SOURCE 3 ORGANISM_TAXID: 272563; SOURCE 4 GENE: CD3205, YP_001089721.1; 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 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3GFA 1 REMARK SEQADV REVDAT 5 24-JUL-19 3GFA 1 REMARK LINK REVDAT 4 25-OCT-17 3GFA 1 REMARK REVDAT 3 13-JUL-11 3GFA 1 VERSN REVDAT 2 23-MAR-11 3GFA 1 TITLE KEYWDS REVDAT 1 17-MAR-09 3GFA 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE NITROREDUCTASE IN COMPLEX WITH JRNL TITL 2 FMN (YP_001089721.1) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.35 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 99648 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4983 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 283 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3077 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 347 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.593 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3627 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2504 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5001 ; 1.504 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6193 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 494 ; 5.547 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;35.420 ;24.765 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 670 ;12.780 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;13.771 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 547 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4085 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 689 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 792 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2835 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1754 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1944 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 276 ; 0.150 ; 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): 29 ; 0.267 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 86 ; 0.225 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 33 ; 0.205 ; 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): 2222 ; 1.932 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 847 ; 1.026 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3550 ; 2.610 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1623 ; 2.093 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1398 ; 2.876 ; 3.000 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): 6794 ; 1.335 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 351 ; 7.409 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6012 ; 3.701 ; 3.000 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 : NULL 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: 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. 4. A FLAVIN MONONUCLEOTIDE (FMN) AND A REMARK 3 CHLORIDE ION IS BOUND TO EACH OF THE TWO ACTIVE SITES WITHIN THE REMARK 3 DIMER. 5.(4S)-2-METHYL-2,4-PENTANEDIOL (MPD) AND GLYCEROL FROM REMARK 3 THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS ARE MODELED INTO REMARK 3 THE STRUCTURE. 6. A MODIFIED FMN RESTRAINTS DICTIONARY WAS USED REMARK 3 DURING THE REFINEMENT TO ALLOW BENDING OF THE FMN RING ALONG THE REMARK 3 N5-N10 VIRTUAL AXIS. THIS RESULTS IN AN IMPROVED FIT BETWEEN THE REMARK 3 FMN COORDINATE MODEL AND ELECTRON DENSITY. REMARK 4 REMARK 4 3GFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97831,0.97870 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) 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 : 99649 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 29.988 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 3.9380 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 FOR SHELL : 1.500 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 (%): 52.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 43.1000% 2-METHYL-2,4-PENTANEDIOL, REMARK 280 0.1M PHOSPHATE-CITRATE PH 3.7, NANODROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.66800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.94550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.66800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 54.94550 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 300 REMARK: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN REMARK 300 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: 10960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL 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 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 220 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 GLY B 0 REMARK 465 MSE B 1 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 MSE A 1 CG SE CE REMARK 470 ILE A 2 CB CG1 CG2 CD1 REMARK 470 SER A 3 OG REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 14 CE NZ REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 LYS A 52 CE NZ REMARK 470 GLU A 55 CD OE1 OE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LYS A 63 CD CE NZ REMARK 470 GLU A 141 CD OE1 OE2 REMARK 470 GLU A 181 CD OE1 OE2 REMARK 470 ILE B 2 CG1 CG2 CD1 REMARK 470 SER B 3 OG REMARK 470 LYS B 8 CD CE NZ REMARK 470 LYS B 14 NZ REMARK 470 LYS B 52 CE NZ REMARK 470 LYS B 59 CD CE NZ REMARK 470 LYS B 63 NZ REMARK 470 ARG B 184 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 41 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391649 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3GFA A 1 197 UNP Q17ZU8 Q17ZU8_CLOD6 1 197 DBREF 3GFA B 1 197 UNP Q17ZU8 Q17ZU8_CLOD6 1 197 SEQADV 3GFA GLY A 0 UNP Q17ZU8 EXPRESSION TAG SEQADV 3GFA GLY B 0 UNP Q17ZU8 EXPRESSION TAG SEQRES 1 A 198 GLY MSE ILE SER ASP SER ILE SER LYS ARG ARG SER ILE SEQRES 2 A 198 ARG LYS TYR LYS ASN GLN SER ILE SER HIS GLU THR ILE SEQRES 3 A 198 GLU LYS ILE ILE GLU ALA GLY ILE ASN ALA PRO SER SER SEQRES 4 A 198 LYS ASN ARG GLN PRO TRP ARG PHE VAL VAL ILE THR GLU SEQRES 5 A 198 LYS GLU LYS GLU SER MSE LEU LYS ALA MSE SER LYS GLY SEQRES 6 A 198 ILE GLN ASN GLU ILE ASN ASP ASN GLY LEU LEU PRO GLY SEQRES 7 A 198 SER ARG GLN HIS ILE ALA GLY ALA ASN TYR THR VAL GLU SEQRES 8 A 198 ILE MSE LYS GLN ALA PRO VAL THR ILE PHE ILE LEU ASN SEQRES 9 A 198 ILE LEU GLY LYS SER PRO LEU GLU LYS LEU SER PRO GLU SEQRES 10 A 198 GLU ARG PHE TYR GLU MSE ALA ASN MSE GLN SER ILE GLY SEQRES 11 A 198 ALA ALA ILE GLN ASN MSE SER LEU THR ALA VAL GLU LEU SEQRES 12 A 198 GLY LEU GLY SER LEU TRP ILE CYS ASP VAL TYR PHE ALA SEQRES 13 A 198 TYR ARG GLU LEU CYS GLU TRP LEU ASN THR ASP SER GLN SEQRES 14 A 198 LEU VAL ALA ALA ILE SER LEU GLY TYR PRO ASP GLU GLU SEQRES 15 A 198 PRO SER ARG ARG PRO ARG LEU GLN LEU SER ASP VAL THR SEQRES 16 A 198 GLU TRP ARG SEQRES 1 B 198 GLY MSE ILE SER ASP SER ILE SER LYS ARG ARG SER ILE SEQRES 2 B 198 ARG LYS TYR LYS ASN GLN SER ILE SER HIS GLU THR ILE SEQRES 3 B 198 GLU LYS ILE ILE GLU ALA GLY ILE ASN ALA PRO SER SER SEQRES 4 B 198 LYS ASN ARG GLN PRO TRP ARG PHE VAL VAL ILE THR GLU SEQRES 5 B 198 LYS GLU LYS GLU SER MSE LEU LYS ALA MSE SER LYS GLY SEQRES 6 B 198 ILE GLN ASN GLU ILE ASN ASP ASN GLY LEU LEU PRO GLY SEQRES 7 B 198 SER ARG GLN HIS ILE ALA GLY ALA ASN TYR THR VAL GLU SEQRES 8 B 198 ILE MSE LYS GLN ALA PRO VAL THR ILE PHE ILE LEU ASN SEQRES 9 B 198 ILE LEU GLY LYS SER PRO LEU GLU LYS LEU SER PRO GLU SEQRES 10 B 198 GLU ARG PHE TYR GLU MSE ALA ASN MSE GLN SER ILE GLY SEQRES 11 B 198 ALA ALA ILE GLN ASN MSE SER LEU THR ALA VAL GLU LEU SEQRES 12 B 198 GLY LEU GLY SER LEU TRP ILE CYS ASP VAL TYR PHE ALA SEQRES 13 B 198 TYR ARG GLU LEU CYS GLU TRP LEU ASN THR ASP SER GLN SEQRES 14 B 198 LEU VAL ALA ALA ILE SER LEU GLY TYR PRO ASP GLU GLU SEQRES 15 B 198 PRO SER ARG ARG PRO ARG LEU GLN LEU SER ASP VAL THR SEQRES 16 B 198 GLU TRP ARG MODRES 3GFA MSE A 1 MET SELENOMETHIONINE MODRES 3GFA MSE A 57 MET SELENOMETHIONINE MODRES 3GFA MSE A 61 MET SELENOMETHIONINE MODRES 3GFA MSE A 92 MET SELENOMETHIONINE MODRES 3GFA MSE A 122 MET SELENOMETHIONINE MODRES 3GFA MSE A 125 MET SELENOMETHIONINE MODRES 3GFA MSE A 135 MET SELENOMETHIONINE MODRES 3GFA MSE B 57 MET SELENOMETHIONINE MODRES 3GFA MSE B 61 MET SELENOMETHIONINE MODRES 3GFA MSE B 92 MET SELENOMETHIONINE MODRES 3GFA MSE B 122 MET SELENOMETHIONINE MODRES 3GFA MSE B 125 MET SELENOMETHIONINE MODRES 3GFA MSE B 135 MET SELENOMETHIONINE HET MSE A 1 5 HET MSE A 57 13 HET MSE A 61 13 HET MSE A 92 8 HET MSE A 122 8 HET MSE A 125 13 HET MSE A 135 13 HET MSE B 57 13 HET MSE B 61 13 HET MSE B 92 8 HET MSE B 122 8 HET MSE B 125 13 HET MSE B 135 8 HET FMN A 200 31 HET CL A 198 1 HET GOL A 199 12 HET GOL A 201 6 HET GOL A 202 6 HET FMN B 200 31 HET CL B 198 1 HET MPD B 199 8 HET MRD B 201 8 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 13(C5 H11 N O2 SE) FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 CL 2(CL 1-) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 10 MPD C6 H14 O2 FORMUL 11 MRD C6 H14 O2 FORMUL 12 HOH *347(H2 O) HELIX 1 1 MSE A 1 ARG A 9 1 9 HELIX 2 2 SER A 21 ASN A 34 1 14 HELIX 3 3 SER A 37 ARG A 41 5 5 HELIX 4 4 GLU A 53 ASN A 70 1 18 HELIX 5 5 LEU A 75 GLN A 80 5 6 HELIX 6 6 HIS A 81 ALA A 95 1 15 HELIX 7 7 SER A 114 LEU A 142 1 29 HELIX 8 8 CYS A 150 PHE A 154 5 5 HELIX 9 9 ALA A 155 ASN A 164 1 10 HELIX 10 10 GLN A 189 VAL A 193 1 5 HELIX 11 11 ILE B 2 ARG B 9 1 8 HELIX 12 12 SER B 21 ASN B 34 1 14 HELIX 13 13 SER B 37 ARG B 41 5 5 HELIX 14 14 THR B 50 ASN B 70 1 21 HELIX 15 15 LEU B 75 GLN B 80 5 6 HELIX 16 16 HIS B 81 ALA B 95 1 15 HELIX 17 17 SER B 114 LEU B 142 1 29 HELIX 18 18 CYS B 150 PHE B 154 5 5 HELIX 19 19 ALA B 155 ASN B 164 1 10 HELIX 20 20 GLN B 189 VAL B 193 1 5 SHEET 1 A 5 GLY A 145 ILE A 149 0 SHEET 2 A 5 GLN A 168 GLY A 176 -1 O GLY A 176 N GLY A 145 SHEET 3 A 5 VAL A 97 ASN A 103 -1 N ILE A 101 O ALA A 171 SHEET 4 A 5 TRP A 44 ILE A 49 -1 N ARG A 45 O LEU A 102 SHEET 5 A 5 THR B 194 ARG B 197 1 O ARG B 197 N VAL A 48 SHEET 1 B 5 THR A 194 ARG A 197 0 SHEET 2 B 5 TRP B 44 ILE B 49 1 O VAL B 48 N ARG A 197 SHEET 3 B 5 VAL B 97 ASN B 103 -1 O THR B 98 N ILE B 49 SHEET 4 B 5 GLN B 168 GLY B 176 -1 O ALA B 171 N ILE B 101 SHEET 5 B 5 GLY B 145 ILE B 149 -1 N GLY B 145 O GLY B 176 LINK C MSE A 1 N ILE A 2 1555 1555 1.32 LINK C SER A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N LEU A 58 1555 1555 1.33 LINK C ALA A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N SER A 62 1555 1555 1.33 LINK C ILE A 91 N MSE A 92 1555 1555 1.33 LINK C MSE A 92 N LYS A 93 1555 1555 1.33 LINK C GLU A 121 N MSE A 122 1555 1555 1.33 LINK C MSE A 122 N ALA A 123 1555 1555 1.32 LINK C ASN A 124 N MSE A 125 1555 1555 1.34 LINK C MSE A 125 N GLN A 126 1555 1555 1.32 LINK C ASN A 134 N MSE A 135 1555 1555 1.33 LINK C MSE A 135 N SER A 136 1555 1555 1.32 LINK C SER B 56 N MSE B 57 1555 1555 1.32 LINK C MSE B 57 N LEU B 58 1555 1555 1.33 LINK C ALA B 60 N MSE B 61 1555 1555 1.32 LINK C MSE B 61 N SER B 62 1555 1555 1.33 LINK C ILE B 91 N MSE B 92 1555 1555 1.33 LINK C MSE B 92 N LYS B 93 1555 1555 1.32 LINK C GLU B 121 N MSE B 122 1555 1555 1.33 LINK C MSE B 122 N ALA B 123 1555 1555 1.33 LINK C ASN B 124 N MSE B 125 1555 1555 1.33 LINK C MSE B 125 N GLN B 126 1555 1555 1.33 LINK C ASN B 134 N MSE B 135 1555 1555 1.34 LINK C MSE B 135 N SER B 136 1555 1555 1.34 SITE 1 AC1 23 ARG A 9 ARG A 10 SER A 11 ARG A 13 SITE 2 AC1 23 THR A 88 LEU A 147 TRP A 148 ILE A 149 SITE 3 AC1 23 CYS A 150 ASP A 151 ARG A 185 ARG A 187 SITE 4 AC1 23 HOH A 222 HOH A 224 HOH A 250 PRO B 36 SITE 5 AC1 23 SER B 37 SER B 38 ASN B 40 ALA B 123 SITE 6 AC1 23 SER B 127 CL B 198 HOH B 287 SITE 1 AC2 3 LYS A 39 HOH A 271 FMN B 200 SITE 1 AC3 8 LEU A 105 GLY A 106 LYS A 107 GLU A 111 SITE 2 AC3 8 LYS A 112 HOH A 333 HOH A 335 HOH A 344 SITE 1 AC4 4 LEU A 58 SER A 62 GLU A 90 LYS A 93 SITE 1 AC5 9 ARG A 45 ILE A 104 THR A 165 ASP A 166 SITE 2 AC5 9 SER A 167 HOH A 275 HOH A 285 HOH A 343 SITE 3 AC5 9 HOH B 235 SITE 1 AC6 24 PRO A 36 SER A 37 SER A 38 ASN A 40 SITE 2 AC6 24 GLN A 126 SER A 127 CL A 198 ARG B 9 SITE 3 AC6 24 ARG B 10 SER B 11 ARG B 13 THR B 88 SITE 4 AC6 24 LEU B 147 TRP B 148 ILE B 149 CYS B 150 SITE 5 AC6 24 ASP B 151 ARG B 185 ARG B 187 HOH B 217 SITE 6 AC6 24 HOH B 236 HOH B 258 HOH B 269 HOH B 272 SITE 1 AC7 3 FMN A 200 LYS B 39 HOH B 361 SITE 1 AC8 8 LEU A 75 CYS A 150 ASP A 151 PHE A 154 SITE 2 AC8 8 LYS B 39 PHE B 119 TYR B 120 HOH B 287 SITE 1 AC9 8 LYS A 39 ARG A 41 PHE A 119 TYR A 120 SITE 2 AC9 8 CYS B 150 ASP B 151 PHE B 154 HOH B 272 CRYST1 73.336 109.891 60.635 90.00 104.84 90.00 C 1 2 1 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 0.013636 0.000000 0.003613 0.00000 SCALE2 0.000000 0.009100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017061 0.00000 HETATM 1 N MSE A 1 16.959 59.879 -10.809 1.00 39.81 N ANISOU 1 N MSE A 1 5119 5070 4934 60 -21 -91 N HETATM 2 CA MSE A 1 16.040 60.675 -9.931 1.00 38.12 C ANISOU 2 CA MSE A 1 5058 4813 4612 -12 -57 -109 C HETATM 3 C MSE A 1 16.137 60.262 -8.457 1.00 36.85 C ANISOU 3 C MSE A 1 4961 4584 4456 -102 22 -149 C HETATM 4 O MSE A 1 15.869 59.109 -8.055 1.00 36.99 O ANISOU 4 O MSE A 1 4981 4681 4391 -362 71 -369 O HETATM 5 CB MSE A 1 14.594 60.533 -10.377 1.00 39.87 C ANISOU 5 CB MSE A 1 5121 5044 4980 -22 -6 -76 C