HEADER OXIDOREDUCTASE 21-MAY-09 3HJ9 TITLE CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE (REUT_A1228) FROM TITLE 2 RALSTONIA EUTROPHA JMP134 AT 2.00 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXIDOREDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA EUTROPHA; SOURCE 3 ORGANISM_TAXID: 264198; SOURCE 4 STRAIN: JMP134; SOURCE 5 GENE: REUT_A1228, YP_295443.1; 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: 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 3HJ9 1 REMARK SEQADV LINK REVDAT 5 24-JUL-19 3HJ9 1 REMARK LINK REVDAT 4 01-NOV-17 3HJ9 1 REMARK REVDAT 3 13-JUL-11 3HJ9 1 VERSN REVDAT 2 23-MAR-11 3HJ9 1 TITLE KEYWDS REVDAT 1 16-JUN-09 3HJ9 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF OXIDOREDUCTASE (YP_295443.1) FROM JRNL TITL 2 RALSTONIA EUTROPHA JMP134 AT 2.00 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33851 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1715 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2299 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3231 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.67000 REMARK 3 B22 (A**2) : -1.67000 REMARK 3 B33 (A**2) : 2.51000 REMARK 3 B12 (A**2) : -0.84000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.948 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3463 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2354 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4743 ; 1.736 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5734 ; 1.378 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 4.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;31.933 ;22.662 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 545 ;11.602 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;13.849 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 519 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3863 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 683 ; 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): 2163 ; 1.166 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 863 ; 0.260 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3470 ; 1.899 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1300 ; 1.251 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1260 ; 1.915 ; 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): 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 2 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): -20.1126 52.0091 7.0021 REMARK 3 T TENSOR REMARK 3 T11: 0.0583 T22: 0.0148 REMARK 3 T33: 0.0044 T12: -0.0183 REMARK 3 T13: 0.0002 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.2017 L22: 1.8790 REMARK 3 L33: 2.0064 L12: -0.1332 REMARK 3 L13: -0.5132 L23: -0.0937 REMARK 3 S TENSOR REMARK 3 S11: -0.0402 S12: 0.1088 S13: 0.0675 REMARK 3 S21: -0.1179 S22: 0.0452 S23: -0.0585 REMARK 3 S31: -0.0593 S32: 0.0617 S33: -0.0050 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 7 B 216 REMARK 3 ORIGIN FOR THE GROUP (A): -32.8998 41.5341 25.6409 REMARK 3 T TENSOR REMARK 3 T11: 0.0618 T22: 0.0518 REMARK 3 T33: 0.0146 T12: -0.0207 REMARK 3 T13: -0.0012 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.6264 L22: 2.4878 REMARK 3 L33: 1.9209 L12: 0.5239 REMARK 3 L13: -0.4282 L23: -0.1221 REMARK 3 S TENSOR REMARK 3 S11: 0.0492 S12: -0.1613 S13: -0.1055 REMARK 3 S21: 0.1830 S22: -0.0018 S23: 0.0259 REMARK 3 S31: 0.1599 S32: -0.0925 S33: -0.0474 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 : 1.40 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE REMARK 3 ION (ACT), MG ION, AND 2-METHYL-2,4-PENTANEDIOL (MPD) MOLECULE REMARK 3 FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED. REMARK 3 5. ONE FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED IN EACH REMARK 3 CHAIN BASED ON THE DENSITY. REMARK 4 REMARK 4 3HJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-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) : 0.91837,0.97837 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 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 68.359 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : 0.10500 REMARK 200 FOR THE DATA SET : 5.9250 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : 0.45100 REMARK 200 FOR SHELL : 1.400 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 (%): 50.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1860M MAGNESIUM ACETATE, 13.6000% REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 NANODROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.03667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.51833 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.51833 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.03667 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: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A REMARK 300 DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 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 VAL A 217 REMARK 465 THR A 218 REMARK 465 THR A 219 REMARK 465 THR A 220 REMARK 465 GLN A 221 REMARK 465 ALA A 222 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 ASN B 2 REMARK 465 ASP B 3 REMARK 465 LEU B 4 REMARK 465 LYS B 5 REMARK 465 ARG B 6 REMARK 465 VAL B 217 REMARK 465 THR B 218 REMARK 465 THR B 219 REMARK 465 THR B 220 REMARK 465 GLN B 221 REMARK 465 ALA B 222 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 13 CG CD CE NZ REMARK 470 GLU A 53 CD OE1 OE2 REMARK 470 GLN A 57 CD OE1 NE2 REMARK 470 GLU A 149 CD OE1 OE2 REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 GLN B 57 CD OE1 NE2 REMARK 470 LEU B 78 CG CD1 CD2 REMARK 470 ARG B 190 CD NE CZ NH1 NH2 REMARK 470 GLU B 200 CG CD OE1 OE2 REMARK 470 ARG B 212 NE CZ NH1 NH2 REMARK 470 HIS B 216 CG ND1 CD2 CE1 NE2 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 B 105 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 117 NE - CZ - NH1 ANGL. DEV. = 3.5 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 THR A 36 -82.79 -80.00 REMARK 500 TYR A 88 14.75 55.19 REMARK 500 LYS B 13 -178.31 -63.63 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 MG B 223 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 226 O REMARK 620 2 HOH B 228 O 164.3 REMARK 620 3 HOH B 229 O 79.7 85.2 REMARK 620 4 HOH B 235 O 86.3 94.3 76.2 REMARK 620 5 HOH B 239 O 86.5 88.9 88.4 163.9 REMARK 620 6 HOH B 240 O 91.1 104.4 167.8 95.4 99.0 REMARK 620 N 1 2 3 4 5 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 ACT A 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 224 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 MG B 223 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391221 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3HJ9 A 1 222 UNP Q472T4 Q472T4_RALEJ 1 222 DBREF 3HJ9 B 1 222 UNP Q472T4 Q472T4_RALEJ 1 222 SEQADV 3HJ9 GLY A 0 UNP Q472T4 EXPRESSION TAG SEQADV 3HJ9 GLY B 0 UNP Q472T4 EXPRESSION TAG SEQRES 1 A 223 GLY MSE ASN ASP LEU LYS ARG LEU PRO TYR GLU PRO VAL SEQRES 2 A 223 LYS GLY LEU LEU PRO ARG PRO ALA VAL GLY THR SER GLU SEQRES 3 A 223 ARG VAL ILE THR LEU PRO GLU PRO ASP ARG THR SER GLY SEQRES 4 A 223 MSE PRO LEU MSE GLY THR LEU TRP LEU ARG LYS SER THR SEQRES 5 A 223 ARG GLU PHE ASP GLN GLN PRO LEU PRO LEU LYS GLN LEU SEQRES 6 A 223 SER GLU LEU LEU TRP ALA ALA ALA GLY VAL ASN ARG SER SEQRES 7 A 223 LEU GLY GLY GLY ARG THR ALA PRO SER PRO TYR GLY GLU SEQRES 8 A 223 THR VAL ILE ASP VAL TYR VAL ALA LEU PRO ALA GLY LEU SEQRES 9 A 223 TYR ARG TYR ASP PRO VAL HIS HIS CYS LEU GLU LEU LYS SEQRES 10 A 223 ARG ALA ALA ASP LEU ARG SER MSE THR GLY TYR GLN ASP SEQRES 11 A 223 PHE VAL GLY MSE ALA PRO LEU ASP LEU VAL PHE VAL ALA SEQRES 12 A 223 ASN HIS GLY ARG MSE GLN GLU MSE PRO PRO LYS LEU ARG SEQRES 13 A 223 GLU THR PHE SER ALA ALA ALA ALA GLY ALA MSE ALA GLU SEQRES 14 A 223 ASN ALA TYR LEU TYR CYS ALA SER ALA GLY LEU GLY ALA SEQRES 15 A 223 VAL VAL ARG GLY TRP LEU ASN ARG ARG GLN LEU ALA GLU SEQRES 16 A 223 HIS MSE SER LEU ASN GLU ASP GLU GLU PRO ILE LEU SER SEQRES 17 A 223 GLN THR ILE GLY ARG ALA ALA SER HIS VAL THR THR THR SEQRES 18 A 223 GLN ALA SEQRES 1 B 223 GLY MSE ASN ASP LEU LYS ARG LEU PRO TYR GLU PRO VAL SEQRES 2 B 223 LYS GLY LEU LEU PRO ARG PRO ALA VAL GLY THR SER GLU SEQRES 3 B 223 ARG VAL ILE THR LEU PRO GLU PRO ASP ARG THR SER GLY SEQRES 4 B 223 MSE PRO LEU MSE GLY THR LEU TRP LEU ARG LYS SER THR SEQRES 5 B 223 ARG GLU PHE ASP GLN GLN PRO LEU PRO LEU LYS GLN LEU SEQRES 6 B 223 SER GLU LEU LEU TRP ALA ALA ALA GLY VAL ASN ARG SER SEQRES 7 B 223 LEU GLY GLY GLY ARG THR ALA PRO SER PRO TYR GLY GLU SEQRES 8 B 223 THR VAL ILE ASP VAL TYR VAL ALA LEU PRO ALA GLY LEU SEQRES 9 B 223 TYR ARG TYR ASP PRO VAL HIS HIS CYS LEU GLU LEU LYS SEQRES 10 B 223 ARG ALA ALA ASP LEU ARG SER MSE THR GLY TYR GLN ASP SEQRES 11 B 223 PHE VAL GLY MSE ALA PRO LEU ASP LEU VAL PHE VAL ALA SEQRES 12 B 223 ASN HIS GLY ARG MSE GLN GLU MSE PRO PRO LYS LEU ARG SEQRES 13 B 223 GLU THR PHE SER ALA ALA ALA ALA GLY ALA MSE ALA GLU SEQRES 14 B 223 ASN ALA TYR LEU TYR CYS ALA SER ALA GLY LEU GLY ALA SEQRES 15 B 223 VAL VAL ARG GLY TRP LEU ASN ARG ARG GLN LEU ALA GLU SEQRES 16 B 223 HIS MSE SER LEU ASN GLU ASP GLU GLU PRO ILE LEU SER SEQRES 17 B 223 GLN THR ILE GLY ARG ALA ALA SER HIS VAL THR THR THR SEQRES 18 B 223 GLN ALA MODRES 3HJ9 MSE A 39 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 42 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 124 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 133 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 147 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 150 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 166 MET SELENOMETHIONINE MODRES 3HJ9 MSE A 196 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 39 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 42 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 124 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 133 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 147 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 150 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 166 MET SELENOMETHIONINE MODRES 3HJ9 MSE B 196 MET SELENOMETHIONINE HET MSE A 39 8 HET MSE A 42 8 HET MSE A 124 13 HET MSE A 133 8 HET MSE A 147 8 HET MSE A 150 8 HET MSE A 166 8 HET MSE A 196 8 HET MSE B 39 8 HET MSE B 42 8 HET MSE B 124 13 HET MSE B 133 8 HET MSE B 147 8 HET MSE B 150 13 HET MSE B 166 8 HET MSE B 196 8 HET FMN A 300 31 HET ACT A 223 4 HET MPD A 224 8 HET FMN B 300 31 HET MG B 223 1 HETNAM MSE SELENOMETHIONINE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ACT ACETATE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MG MAGNESIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 MPD C6 H14 O2 FORMUL 7 MG MG 2+ FORMUL 8 HOH *287(H2 O) HELIX 1 1 ASN A 2 LEU A 7 5 6 HELIX 2 2 PRO A 40 ARG A 48 1 9 HELIX 3 3 PRO A 60 GLY A 73 1 14 HELIX 4 4 SER A 77 GLY A 80 5 4 HELIX 5 5 SER A 86 GLU A 90 5 5 HELIX 6 6 GLY A 145 MSE A 147 5 3 HELIX 7 7 PRO A 151 LYS A 153 5 3 HELIX 8 8 LEU A 154 ALA A 177 1 24 HELIX 9 9 ASN A 188 MSE A 196 1 9 HELIX 10 10 PRO B 40 ARG B 48 1 9 HELIX 11 11 PRO B 60 GLY B 73 1 14 HELIX 12 12 SER B 86 GLU B 90 5 5 HELIX 13 13 GLY B 145 MSE B 147 5 3 HELIX 14 14 PRO B 151 GLY B 178 1 28 HELIX 15 15 ASN B 188 MSE B 196 1 9 SHEET 1 A 2 GLU A 10 PRO A 11 0 SHEET 2 A 2 TYR A 127 GLN A 128 -1 O GLN A 128 N GLU A 10 SHEET 1 B 2 ARG A 18 PRO A 19 0 SHEET 2 B 2 ALA A 119 ASP A 120 -1 O ASP A 120 N ARG A 18 SHEET 1 C 7 VAL A 27 THR A 29 0 SHEET 2 C 7 CYS A 112 ARG A 117 -1 O LEU A 113 N ILE A 28 SHEET 3 C 7 GLY A 102 ASP A 107 -1 N LEU A 103 O LYS A 116 SHEET 4 C 7 ILE A 93 LEU A 99 -1 N VAL A 97 O TYR A 104 SHEET 5 C 7 LEU A 136 ASN A 143 -1 O VAL A 141 N ASP A 94 SHEET 6 C 7 GLU A 202 GLY A 211 -1 O GLU A 203 N ALA A 142 SHEET 7 C 7 GLY A 180 ARG A 184 -1 N GLY A 180 O GLY A 211 SHEET 1 D 2 VAL A 74 ARG A 76 0 SHEET 2 D 2 GLY A 81 ARG A 82 -1 O GLY A 81 N ASN A 75 SHEET 1 E 2 GLU B 10 PRO B 11 0 SHEET 2 E 2 TYR B 127 GLN B 128 -1 O GLN B 128 N GLU B 10 SHEET 1 F 2 ARG B 18 PRO B 19 0 SHEET 2 F 2 ALA B 119 ASP B 120 -1 O ASP B 120 N ARG B 18 SHEET 1 G 7 VAL B 27 THR B 29 0 SHEET 2 G 7 CYS B 112 ARG B 117 -1 O LEU B 113 N ILE B 28 SHEET 3 G 7 GLY B 102 ASP B 107 -1 N LEU B 103 O LYS B 116 SHEET 4 G 7 ILE B 93 LEU B 99 -1 N VAL B 97 O TYR B 104 SHEET 5 G 7 LEU B 136 ASN B 143 -1 O VAL B 141 N ASP B 94 SHEET 6 G 7 GLU B 202 GLY B 211 -1 O LEU B 206 N PHE B 140 SHEET 7 G 7 GLY B 180 ARG B 184 -1 N ARG B 184 O SER B 207 SHEET 1 H 2 VAL B 74 ARG B 76 0 SHEET 2 H 2 GLY B 81 ARG B 82 -1 O GLY B 81 N ASN B 75 LINK C GLY A 38 N MSE A 39 1555 1555 1.33 LINK C MSE A 39 N PRO A 40 1555 1555 1.36 LINK C LEU A 41 N MSE A 42 1555 1555 1.34 LINK C MSE A 42 N GLY A 43 1555 1555 1.34 LINK C SER A 123 N MSE A 124 1555 1555 1.34 LINK C MSE A 124 N THR A 125 1555 1555 1.34 LINK C GLY A 132 N MSE A 133 1555 1555 1.33 LINK C MSE A 133 N ALA A 134 1555 1555 1.32 LINK C ARG A 146 N MSE A 147 1555 1555 1.34 LINK C MSE A 147 N GLN A 148 1555 1555 1.34 LINK C GLU A 149 N MSE A 150 1555 1555 1.35 LINK C MSE A 150 N PRO A 151 1555 1555 1.36 LINK C ALA A 165 N MSE A 166 1555 1555 1.33 LINK C MSE A 166 N ALA A 167 1555 1555 1.33 LINK C HIS A 195 N MSE A 196 1555 1555 1.34 LINK C MSE A 196 N SER A 197 1555 1555 1.35 LINK C GLY B 38 N MSE B 39 1555 1555 1.33 LINK C MSE B 39 N PRO B 40 1555 1555 1.34 LINK C LEU B 41 N MSE B 42 1555 1555 1.33 LINK C MSE B 42 N GLY B 43 1555 1555 1.34 LINK C SER B 123 N MSE B 124 1555 1555 1.33 LINK C MSE B 124 N THR B 125 1555 1555 1.33 LINK C GLY B 132 N MSE B 133 1555 1555 1.33 LINK C MSE B 133 N ALA B 134 1555 1555 1.33 LINK C ARG B 146 N MSE B 147 1555 1555 1.34 LINK C MSE B 147 N GLN B 148 1555 1555 1.34 LINK C GLU B 149 N MSE B 150 1555 1555 1.33 LINK C MSE B 150 N PRO B 151 1555 1555 1.35 LINK C ALA B 165 N MSE B 166 1555 1555 1.31 LINK C MSE B 166 N ALA B 167 1555 1555 1.34 LINK C HIS B 195 N MSE B 196 1555 1555 1.33 LINK C MSE B 196 N SER B 197 1555 1555 1.35 LINK MG MG B 223 O HOH B 226 1555 1555 1.96 LINK MG MG B 223 O HOH B 228 1555 1555 1.94 LINK MG MG B 223 O HOH B 229 1555 1555 2.05 LINK MG MG B 223 O HOH B 235 1555 1555 2.02 LINK MG MG B 223 O HOH B 239 1555 1555 1.97 LINK MG MG B 223 O HOH B 240 1555 1555 1.98 SITE 1 AC1 22 ARG A 48 LYS A 49 SER A 50 ARG A 52 SITE 2 AC1 22 ASP A 129 VAL A 131 VAL A 183 ARG A 184 SITE 3 AC1 22 GLY A 185 TRP A 186 ACT A 223 HOH A 236 SITE 4 AC1 22 HOH A 247 HOH A 248 HOH A 254 HOH A 356 SITE 5 AC1 22 ARG B 76 PRO B 85 SER B 86 GLY B 89 SITE 6 AC1 22 PHE B 158 ALA B 161 SITE 1 AC2 5 TYR A 9 FMN A 300 HOH A 356 TYR B 88 SITE 2 AC2 5 PHE B 158 SITE 1 AC3 6 LEU A 7 ARG A 26 ARG A 105 LEU A 115 SITE 2 AC3 6 LYS A 116 HOH A 290 SITE 1 AC4 21 ARG A 76 PRO A 85 SER A 86 PRO A 87 SITE 2 AC4 21 GLY A 89 TYR B 9 ARG B 48 LYS B 49 SITE 3 AC4 21 SER B 50 ARG B 52 ASP B 129 VAL B 131 SITE 4 AC4 21 VAL B 182 VAL B 183 ARG B 184 GLY B 185 SITE 5 AC4 21 TRP B 186 HOH B 244 HOH B 251 HOH B 253 SITE 6 AC4 21 HOH B 316 SITE 1 AC5 6 HOH B 226 HOH B 228 HOH B 229 HOH B 235 SITE 2 AC5 6 HOH B 239 HOH B 240 CRYST1 78.865 78.865 136.555 90.00 90.00 120.00 P 32 2 1 12 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 0.012680 0.007321 0.000000 0.00000 SCALE2 0.000000 0.014641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007323 0.00000