HEADER OXIDOREDUCTASE 20-APR-09 3H4O TITLE CRYSTAL STRUCTURE OF A NITROREDUCTASE FAMILY PROTEIN (CD3355) FROM TITLE 2 CLOSTRIDIUM DIFFICILE 630 AT 1.50 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROREDUCTASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM DIFFICILE 630; SOURCE 3 ORGANISM_TAXID: 272563; SOURCE 4 GENE: CD3355, YP_001089872.1; 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 5 01-FEB-23 3H4O 1 REMARK SEQADV REVDAT 4 24-JUL-19 3H4O 1 REMARK LINK REVDAT 3 25-OCT-17 3H4O 1 REMARK REVDAT 2 23-MAR-11 3H4O 1 TITLE KEYWDS REVDAT 1 19-MAY-09 3H4O 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF NITROREDUCTASE FAMILY PROTEIN JRNL TITL 2 (YP_001089872.1) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.50 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 32400 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) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1637 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2187 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1381 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.112 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1549 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1078 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2114 ; 1.540 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2652 ; 0.959 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 191 ; 5.764 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;35.170 ;24.627 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 293 ;12.883 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;10.705 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 233 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1702 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 283 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 300 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1154 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 770 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 766 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 210 ; 0.145 ; 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): 12 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 67 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.171 ; 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): 964 ; 1.865 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 360 ; 0.425 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1519 ; 2.437 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 684 ; 4.034 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 595 ; 6.186 ;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 : 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 3. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS REMARK 3 MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT. THE FMN REMARK 3 RESTRAINTS WERE CHANGED TO ALLOW BENDING OF THE ISOALLOXAZINE REMARK 3 RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT REMARK 3 BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY. 4. (4S)- AND REMARK 3 (4R)-2-METHYL-2,4-PENTANEDIOL (MPD / MRD) MOLECULES WERE MODELED REMARK 3 BASED ON THE CRYOPROTECTION CONDITION. REMARK 4 REMARK 4 3H4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.91837,0.97840,0.97883 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32401 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.348 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS REMARK 200 SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35.0000% DIOXANE, 0.001 M FLAVIN REMARK 280 MONONUCLEOTIDE (FMN), NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 38.94850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.74350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.94850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.74350 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: SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING REMARK 300 SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION REMARK 300 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: 9210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 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 -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 ASP A -15 REMARK 465 LYS A -14 REMARK 465 ILE A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 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 LYS A 158 CE NZ 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 9 O HOH A 369 2.16 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 155 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -3.3 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 148 -136.06 -125.57 REMARK 500 GLU A 170 -43.14 73.45 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 MPD A 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 174 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391667 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG FOLLOWED BY THE TARGET SEQUENCE. DBREF 3H4O A 1 172 UNP Q180K0 Q180K0_CLOD6 1 172 SEQADV 3H4O MSE A -18 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O GLY A -17 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O SER A -16 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O ASP A -15 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O LYS A -14 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O ILE A -13 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -12 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -11 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -10 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -9 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -8 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O HIS A -7 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O GLU A -6 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O ASN A -5 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O LEU A -4 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O TYR A -3 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O PHE A -2 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O GLN A -1 UNP Q180K0 EXPRESSION TAG SEQADV 3H4O GLY A 0 UNP Q180K0 EXPRESSION TAG SEQRES 1 A 191 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS GLU SEQRES 2 A 191 ASN LEU TYR PHE GLN GLY MSE ASN PHE VAL GLU LEU ALA SEQRES 3 A 191 LYS LYS ARG TYR SER CYS ARG ASN TYR GLN ASP ARG LYS SEQRES 4 A 191 VAL GLU LYS GLU LYS LEU GLU LYS VAL LEU ASP VAL ALA SEQRES 5 A 191 ARG ILE ALA PRO THR GLY GLY ASN ARG GLN PRO GLN ARG SEQRES 6 A 191 LEU ILE VAL ILE GLN GLU LYS GLU GLY ILE ASN LYS LEU SEQRES 7 A 191 SER LYS ALA ALA ASN ILE TYR ASP ALA PRO LEU ALA ILE SEQRES 8 A 191 LEU VAL CYS GLY ASP LYS ASP LYS VAL TRP THR ARG PRO SEQRES 9 A 191 PHE ASP GLY LYS GLN LEU THR ASP ILE ASP THR SER ILE SEQRES 10 A 191 VAL THR ASP HIS MSE MSE LEU GLN ALA THR GLU LEU GLY SEQRES 11 A 191 LEU ALA SER VAL TRP VAL CYS TYR PHE ASN PRO ASP ILE SEQRES 12 A 191 ILE ARG GLU GLU PHE SER LEU PRO ASP ASN LEU GLU PRO SEQRES 13 A 191 ILE ASN ILE LEU LEU MSE GLY TYR GLU SER LYS ILE PRO SEQRES 14 A 191 GLU SER PRO GLU ARG HIS GLU LYS THR ARG VAL PRO LEU SEQRES 15 A 191 SER GLU ILE VAL SER TYR GLU THR LEU MODRES 3H4O MSE A 1 MET SELENOMETHIONINE MODRES 3H4O MSE A 103 MET SELENOMETHIONINE MODRES 3H4O MSE A 104 MET SELENOMETHIONINE MODRES 3H4O MSE A 143 MET SELENOMETHIONINE HET MSE A 1 5 HET MSE A 103 8 HET MSE A 104 8 HET MSE A 143 16 HET FMN A 300 31 HET MPD A 173 8 HET MRD A 174 8 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 MPD C6 H14 O2 FORMUL 4 MRD C6 H14 O2 FORMUL 5 HOH *294(H2 O) HELIX 1 1 ASN A 2 ARG A 10 1 9 HELIX 2 2 GLU A 22 ALA A 36 1 15 HELIX 3 3 THR A 38 ARG A 42 5 5 HELIX 4 4 GLU A 52 ALA A 63 1 12 HELIX 5 5 LEU A 91 LEU A 110 1 20 HELIX 6 6 ASN A 121 PHE A 129 1 9 HELIX 7 7 ARG A 155 ARG A 160 1 6 HELIX 8 8 PRO A 162 ILE A 166 5 5 SHEET 1 A 4 GLN A 45 ILE A 50 0 SHEET 2 A 4 LEU A 70 ASP A 77 -1 O ALA A 71 N ILE A 50 SHEET 3 A 4 LEU A 135 GLY A 144 -1 O ASN A 139 N VAL A 74 SHEET 4 A 4 ALA A 113 VAL A 117 -1 N VAL A 115 O LEU A 142 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C HIS A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N MSE A 104 1555 1555 1.33 LINK C MSE A 104 N LEU A 105 1555 1555 1.33 LINK C LEU A 142 N AMSE A 143 1555 1555 1.33 LINK C LEU A 142 N BMSE A 143 1555 1555 1.33 LINK C AMSE A 143 N GLY A 144 1555 1555 1.33 LINK C BMSE A 143 N GLY A 144 1555 1555 1.33 SITE 1 AC1 24 ARG A 10 SER A 12 ARG A 14 PRO A 37 SITE 2 AC1 24 THR A 38 GLY A 39 ASN A 41 TYR A 66 SITE 3 AC1 24 ILE A 94 ASP A 95 ILE A 98 VAL A 115 SITE 4 AC1 24 TRP A 116 VAL A 117 CYS A 118 TYR A 119 SITE 5 AC1 24 GLU A 151 ARG A 155 ARG A 160 MPD A 173 SITE 6 AC1 24 HOH A 305 HOH A 320 HOH A 328 HOH A 345 SITE 1 AC2 4 GLY A 40 TRP A 82 HOH A 272 FMN A 300 SITE 1 AC3 7 ALA A 62 ALA A 63 PHE A 86 TYR A 119 SITE 2 AC3 7 HOH A 282 HOH A 324 HOH A 396 CRYST1 77.897 63.487 55.465 90.00 131.11 90.00 C 1 2 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 0.012837 0.000000 0.011203 0.00000 SCALE2 0.000000 0.015751 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023929 0.00000 HETATM 1 N MSE A 1 3.630 45.200 -2.610 1.00 42.84 N HETATM 2 CA MSE A 1 3.078 46.554 -2.970 1.00 39.42 C HETATM 3 C MSE A 1 3.009 47.437 -1.713 1.00 35.46 C HETATM 4 O MSE A 1 2.021 47.393 -0.970 1.00 37.89 O HETATM 5 CB MSE A 1 1.679 46.416 -3.607 1.00 40.79 C