HEADER OXIDOREDUCTASE 14-MAY-10 3N0Q TITLE CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC-RING HYDROXYLATING TITLE 2 DIOXYGENASE (TM1040_3219) FROM SILICIBACTER SP. TM1040 AT 1.80 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AROMATIC-RING HYDROXYLATING DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROBABLE RING HYDROXYLATING ALPHA SUBUNIT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUEGERIA SP. TM1040; SOURCE 3 ORGANISM_TAXID: 292414; SOURCE 4 GENE: BENA, TM1040_3219; 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 RIESKE [2FE-2S] DOMAIN, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 01-FEB-23 3N0Q 1 REMARK SEQADV LINK REVDAT 3 17-JUL-19 3N0Q 1 REMARK LINK REVDAT 2 25-OCT-17 3N0Q 1 REMARK REVDAT 1 09-JUN-10 3N0Q 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC-RING HYDROXYLATING JRNL TITL 2 DIOXYGENASE (TM1040_3219) FROM SILICIBACTER SP. TM1040 AT JRNL TITL 3 1.80 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0073 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48240 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2418 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3327 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3207 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 469 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.42000 REMARK 3 B12 (A**2) : -0.14000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.589 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3447 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2360 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4704 ; 1.475 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5712 ; 1.379 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 433 ; 6.436 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;37.390 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 548 ;12.719 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.806 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 488 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3909 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 1 A 402 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6980 53.3350 2.1870 REMARK 3 T TENSOR REMARK 3 T11: 0.0528 T22: 0.0328 REMARK 3 T33: 0.0169 T12: 0.0132 REMARK 3 T13: 0.0029 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 1.1348 L22: 0.5457 REMARK 3 L33: 0.1740 L12: 0.0288 REMARK 3 L13: -0.0780 L23: 0.0324 REMARK 3 S TENSOR REMARK 3 S11: 0.0168 S12: 0.0452 S13: 0.1146 REMARK 3 S21: -0.0099 S22: 0.0039 S23: 0.0320 REMARK 3 S31: -0.0579 S32: -0.0103 S33: -0.0207 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. 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 4. NICKEL (NI), CHLORIDE (CL) AND TROMETHAMINE (TRS; REMARK 3 TRIS) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM REMARK 3 THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED. 5. AN IRON- REMARK 3 SULPHUR [2FE-2S] CLUSTER HAS BEEN MODELED. 6. THE PRESENCE OF REMARK 3 IRON AND NICKEL HAVE BEEN VERIFIED BY X-RAY FLUORESCENCE AND BY REMARK 3 CALCULATING ANOMALOUS DIFFERENCE FOURIER MAPS FROM DATA REMARK 3 COLLECTED BELOW AND ABOVE THE IRON AND NICKEL K-SHELL ABSORPTION REMARK 3 EDGES. REMARK 4 REMARK 4 3N0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.29 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) : 0.91837,0.97949,0.97895 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 : 48265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.155 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.310 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.160 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23.8000% POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 2000, 0.0100M NICKEL (II) CHLORIDE, 0.1M TRIS REMARK 280 PH 8.29, NANODROP', VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 48.26100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.26100 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 48.26100 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 AND ANALYTICAL SIZE EXCLUSION REMARK 300 CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE REMARK 300 ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIC FORM 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -162.0 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 -0.500000 -0.866025 0.000000 97.53300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 48.76650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 84.46606 REMARK 350 BIOMT3 3 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 HIS A 403 REMARK 465 ALA A 404 REMARK 465 VAL A 405 REMARK 465 ALA A 406 REMARK 465 ALA A 407 REMARK 465 GLU A 408 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 GLU A 264 CG CD OE1 OE2 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 HIS A 2 C - N - CA ANGL. DEV. = 17.8 DEGREES REMARK 500 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -3.8 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 HIS A 2 -6.33 81.77 REMARK 500 SER A 3 -73.94 66.03 REMARK 500 ALA A 44 -71.81 -105.28 REMARK 500 HIS A 85 -81.26 -80.09 REMARK 500 SER A 245 -27.44 -143.64 REMARK 500 ASP A 288 57.73 -95.86 REMARK 500 VAL A 338 -56.00 -124.10 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 502 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 NE2 REMARK 620 2 TRS A 505 O3 89.9 REMARK 620 3 TRS A 505 O2 98.8 86.7 REMARK 620 4 TRS A 505 O1 167.6 78.2 77.4 REMARK 620 5 HOH A 589 O 91.5 176.1 96.7 100.7 REMARK 620 6 HOH A 663 O 95.5 85.0 163.5 86.9 91.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 410 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 83 SG REMARK 620 2 FES A 410 S1 109.8 REMARK 620 3 FES A 410 S2 110.9 104.3 REMARK 620 4 CYS A 103 SG 107.9 109.0 114.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 410 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 ND1 REMARK 620 2 FES A 410 S1 116.2 REMARK 620 3 FES A 410 S2 112.9 105.1 REMARK 620 4 HIS A 106 ND1 91.6 111.1 120.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 201 NE2 REMARK 620 2 HIS A 206 NE2 97.5 REMARK 620 3 ASP A 356 OD1 99.1 87.3 REMARK 620 4 TRS A 504 O3 165.0 88.7 94.9 REMARK 620 5 TRS A 504 O1 91.0 171.5 91.3 83.1 REMARK 620 6 TRS A 504 N 90.0 103.9 164.6 75.2 76.1 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 FES A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 397279 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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 3N0Q A 1 408 UNP Q1GMC3 Q1GMC3_SILST 1 408 SEQADV 3N0Q GLY A 0 UNP Q1GMC3 EXPRESSION TAG SEQRES 1 A 409 GLY MSE HIS SER ASN ILE ASN THR LEU ILE ALA ASN HIS SEQRES 2 A 409 ARG ALA GLY HIS ALA LEU ASP GLN ALA PHE TYR THR ASP SEQRES 3 A 409 ALA GLU VAL PHE GLN THR ASP LEU GLN GLU ILE PHE TYR SEQRES 4 A 409 LYS GLU TRP LEU PHE ALA ILE PRO ALA CYS GLU LEU ASP SEQRES 5 A 409 LYS PRO GLY SER TYR VAL THR HIS GLN VAL GLY ASN TYR SEQRES 6 A 409 ASN VAL ILE ILE VAL ARG GLY ALA ASP ASN VAL ILE ARG SEQRES 7 A 409 ALA PHE HIS ASN ALA CYS ARG HIS ARG GLY SER VAL ILE SEQRES 8 A 409 CYS LYS ALA LYS LYS GLY ASN ASN PRO LYS LEU VAL CYS SEQRES 9 A 409 PRO TYR HIS GLN TRP THR TYR GLU LEU ASP GLY ARG LEU SEQRES 10 A 409 LEU TRP ALA ARG ASP MSE GLY PRO ASP PHE GLU PRO SER SEQRES 11 A 409 ARG HIS GLY LEU LYS THR VAL HIS CYS ARG GLU LEU ALA SEQRES 12 A 409 GLY LEU ILE TYR ILE CYS LEU ALA ASP GLU ALA PRO ASP SEQRES 13 A 409 PHE GLU ARG PHE ALA GLU VAL ALA ARG PRO TYR LEU GLU SEQRES 14 A 409 VAL HIS ASP LEU SER ASN ALA LYS VAL ALA HIS GLU SER SEQRES 15 A 409 SER ILE VAL GLU ARG GLY ASN TRP LYS LEU VAL TRP GLU SEQRES 16 A 409 ASN ASN ARG GLU CYS TYR HIS CYS GLY GLY ASN HIS PRO SEQRES 17 A 409 ALA LEU CYS ARG THR PHE PRO ASP ASP PRO SER VAL THR SEQRES 18 A 409 GLY ILE GLU GLY GLY GLU THR PRO SER ASN LEU GLN ALA SEQRES 19 A 409 HIS PHE ASP ARG CYS GLU GLN ALA GLY MSE PRO SER GLY SEQRES 20 A 409 PHE HIS LEU SER GLY ASP GLY GLN PHE ARG VAL ALA ARG SEQRES 21 A 409 MSE PRO LEU LYS GLU GLY ALA GLU SER TYR THR MSE ASP SEQRES 22 A 409 GLY LYS THR ALA VAL ARG ARG TRP LEU GLY ARG ALA ALA SEQRES 23 A 409 PHE ALA ASP ALA GLY SER LEU LEU LYS PHE HIS TYR PRO SEQRES 24 A 409 THR THR TRP ASN HIS PHE LEU SER ASP HIS SER ILE VAL SEQRES 25 A 409 PHE ARG VAL THR PRO ILE SER PRO THR GLU THR GLU VAL SEQRES 26 A 409 THR THR LYS TRP LEU VAL HIS LYS ASP ALA VAL GLU GLY SEQRES 27 A 409 VAL ASP TYR ASP LEU GLN ARG LEU THR GLU VAL TRP ILE SEQRES 28 A 409 ALA THR ASN ASP GLU ASP ARG GLU VAL VAL GLU PHE ASN SEQRES 29 A 409 GLN MSE GLY ILE ASN SER PRO ALA TYR GLU PRO GLY PRO SEQRES 30 A 409 TYR SER PRO THR GLN GLU SER GLY VAL LEU GLN PHE VAL SEQRES 31 A 409 GLU TRP TYR LEU SER THR LEU LYS ARG ASN SER GLY PRO SEQRES 32 A 409 HIS ALA VAL ALA ALA GLU MODRES 3N0Q MSE A 1 MET SELENOMETHIONINE MODRES 3N0Q MSE A 122 MET SELENOMETHIONINE MODRES 3N0Q MSE A 243 MET SELENOMETHIONINE MODRES 3N0Q MSE A 260 MET SELENOMETHIONINE MODRES 3N0Q MSE A 271 MET SELENOMETHIONINE MODRES 3N0Q MSE A 365 MET SELENOMETHIONINE HET MSE A 1 16 HET MSE A 122 8 HET MSE A 243 13 HET MSE A 260 8 HET MSE A 271 8 HET MSE A 365 8 HET FES A 410 4 HET NI A 501 1 HET NI A 502 1 HET CL A 503 1 HET TRS A 504 8 HET TRS A 505 8 HET GOL A 506 6 HET GOL A 507 6 HETNAM MSE SELENOMETHIONINE HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 FES FE2 S2 FORMUL 3 NI 2(NI 2+) FORMUL 5 CL CL 1- FORMUL 6 TRS 2(C4 H12 N O3 1+) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *469(H2 O) HELIX 1 1 ASN A 4 ASN A 11 1 8 HELIX 2 2 ASP A 19 ASP A 25 1 7 HELIX 3 3 ASP A 25 ILE A 36 1 12 HELIX 4 4 CYS A 48 LEU A 50 5 3 HELIX 5 5 GLU A 127 HIS A 131 5 5 HELIX 6 6 PHE A 156 VAL A 169 1 14 HELIX 7 7 HIS A 170 SER A 173 5 4 HELIX 8 8 ASN A 188 ARG A 197 1 10 HELIX 9 9 HIS A 201 HIS A 206 1 6 HELIX 10 10 ALA A 208 THR A 212 5 5 HELIX 11 11 ASP A 216 GLY A 221 1 6 HELIX 12 12 PRO A 228 ALA A 241 1 14 HELIX 13 13 ASP A 341 ASN A 368 1 28 HELIX 14 14 GLU A 382 GLY A 401 1 20 SHEET 1 A 7 LEU A 42 PRO A 46 0 SHEET 2 A 7 LEU A 144 CYS A 148 -1 O ILE A 145 N ILE A 45 SHEET 3 A 7 THR A 135 LEU A 141 -1 N LEU A 141 O LEU A 144 SHEET 4 A 7 ILE A 76 HIS A 80 -1 N ALA A 78 O VAL A 136 SHEET 5 A 7 TYR A 64 ARG A 70 -1 N ILE A 67 O PHE A 79 SHEET 6 A 7 SER A 55 VAL A 61 -1 N HIS A 59 O VAL A 66 SHEET 7 A 7 LYS A 95 ASN A 97 -1 O GLY A 96 N TYR A 56 SHEET 1 B 3 LEU A 101 VAL A 102 0 SHEET 2 B 3 THR A 109 TYR A 110 -1 O TYR A 110 N LEU A 101 SHEET 3 B 3 LEU A 116 TRP A 118 -1 O TRP A 118 N THR A 109 SHEET 1 C 7 ALA A 175 GLU A 185 0 SHEET 2 C 7 GLU A 321 HIS A 331 -1 O THR A 322 N GLU A 185 SHEET 3 C 7 SER A 309 SER A 318 -1 N SER A 309 O LEU A 329 SHEET 4 C 7 THR A 300 PHE A 304 -1 N HIS A 303 O ILE A 310 SHEET 5 C 7 SER A 291 HIS A 296 -1 N LEU A 292 O PHE A 304 SHEET 6 C 7 PHE A 255 MSE A 260 -1 N ALA A 258 O LEU A 293 SHEET 7 C 7 HIS A 248 LEU A 249 -1 N HIS A 248 O VAL A 257 SSBOND 1 CYS A 199 CYS A 202 1555 1555 2.05 LINK C AMSE A 1 N HIS A 2 1555 1555 1.34 LINK C BMSE A 1 N HIS A 2 1555 1555 1.34 LINK C ASP A 121 N MSE A 122 1555 1555 1.33 LINK C MSE A 122 N GLY A 123 1555 1555 1.33 LINK C GLY A 242 N MSE A 243 1555 1555 1.34 LINK C MSE A 243 N PRO A 244 1555 1555 1.35 LINK C ARG A 259 N MSE A 260 1555 1555 1.32 LINK C MSE A 260 N PRO A 261 1555 1555 1.35 LINK C THR A 270 N MSE A 271 1555 1555 1.32 LINK C MSE A 271 N ASP A 272 1555 1555 1.34 LINK C GLN A 364 N MSE A 365 1555 1555 1.32 LINK C MSE A 365 N GLY A 366 1555 1555 1.33 LINK NE2 HIS A 16 NI NI A 502 1555 1555 2.16 LINK SG CYS A 83 FE1 FES A 410 1555 1555 2.30 LINK ND1 HIS A 85 FE2 FES A 410 1555 1555 2.13 LINK SG CYS A 103 FE1 FES A 410 1555 1555 2.29 LINK ND1 HIS A 106 FE2 FES A 410 1555 1555 2.16 LINK NE2 HIS A 201 NI NI A 501 1555 1555 2.13 LINK NE2 HIS A 206 NI NI A 501 1555 1555 2.13 LINK OD1 ASP A 356 NI NI A 501 1555 1555 2.03 LINK NI NI A 501 O3 TRS A 504 1555 1555 2.06 LINK NI NI A 501 O1 TRS A 504 1555 1555 2.18 LINK NI NI A 501 N TRS A 504 1555 1555 2.38 LINK NI NI A 502 O3 TRS A 505 1555 1555 1.74 LINK NI NI A 502 O2 TRS A 505 1555 1555 2.25 LINK NI NI A 502 O1 TRS A 505 1555 1555 2.34 LINK NI NI A 502 O HOH A 589 1555 1555 2.02 LINK NI NI A 502 O HOH A 663 1555 1555 2.18 CISPEP 1 TYR A 297 PRO A 298 0 9.78 SITE 1 AC1 6 CYS A 83 HIS A 85 ARG A 86 CYS A 103 SITE 2 AC1 6 HIS A 106 TRP A 108 SITE 1 AC2 4 HIS A 201 HIS A 206 ASP A 356 TRS A 504 SITE 1 AC3 4 HIS A 16 TRS A 505 HOH A 589 HOH A 663 SITE 1 AC4 2 ASN A 196 HIS A 303 SITE 1 AC5 13 ASN A 195 ASN A 196 GLU A 198 CYS A 199 SITE 2 AC5 13 HIS A 201 CYS A 202 HIS A 206 PHE A 213 SITE 3 AC5 13 THR A 220 THR A 352 ASP A 356 NI A 501 SITE 4 AC5 13 HOH A 854 SITE 1 AC6 11 ARG A 13 HIS A 16 ARG A 84 ARG A 130 SITE 2 AC6 11 HIS A 131 GLU A 373 PRO A 374 PRO A 376 SITE 3 AC6 11 NI A 502 HOH A 663 HOH A 822 SITE 1 AC7 8 GLY A 71 ALA A 72 ASP A 73 ARG A 77 SITE 2 AC7 8 LEU A 112 ASP A 113 HOH A 714 HOH A 807 SITE 1 AC8 7 HIS A 12 GLU A 390 LYS A 397 HOH A 671 SITE 2 AC8 7 HOH A 786 HOH A 841 HOH A 872 CRYST1 97.533 97.533 96.522 90.00 90.00 120.00 P 63 6 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 0.010253 0.005920 0.000000 0.00000 SCALE2 0.000000 0.011839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010360 0.00000 HETATM 1 N AMSE A 1 39.271 28.920 -16.159 0.50 47.98 N ANISOU 1 N AMSE A 1 5666 6534 6027 -4 24 -1251 N HETATM 2 N BMSE A 1 38.331 28.594 -17.728 0.50 46.97 N ANISOU 2 N BMSE A 1 5510 6520 5815 -18 -2 -1376 N HETATM 3 CA AMSE A 1 37.848 29.366 -16.043 0.50 44.77 C ANISOU 3 CA AMSE A 1 5274 6148 5587 -2 -20 -1211 C HETATM 4 CA BMSE A 1 37.180 28.787 -16.798 0.50 44.64 C ANISOU 4 CA BMSE A 1 5224 6168 5566 -11 -38 -1301 C HETATM 5 C AMSE A 1 37.755 30.772 -16.617 0.50 45.43 C ANISOU 5 C AMSE A 1 5409 6333 5518 1 -32 -1145 C HETATM 6 C BMSE A 1 36.233 29.862 -17.308 0.50 44.27 C ANISOU 6 C BMSE A 1 5212 6213 5395 -9 -77 -1253 C HETATM 7 O AMSE A 1 38.709 31.545 -16.485 0.50 45.81 O ANISOU 7 O AMSE A 1 5491 6393 5518 6 -7 -1083 O HETATM 8 O BMSE A 1 35.140 29.534 -17.753 0.50 44.56 O ANISOU 8 O BMSE A 1 5223 6278 5429 -14 -112 -1305 O HETATM 9 CB AMSE A 1 37.450 29.386 -14.560 0.50 44.42 C ANISOU 9 CB AMSE A 1 5240 6001 5636 6 -29 -1116 C HETATM 10 CB BMSE A 1 37.684 29.149 -15.418 0.50 40.65 C ANISOU 10 CB BMSE A 1 4747 5572 5124 0 -22 -1186 C HETATM 11 CG AMSE A 1 35.985 29.191 -14.245 0.50 43.21 C ANISOU 11 CG AMSE A 1 5072 5825 5519 6 -66 -1109 C HETATM 12 CG BMSE A 1 38.968 29.945 -15.465 0.50 37.83 C ANISOU 12 CG BMSE A 1 4427 5244 4701 5 9 -1136 C HETATM 13 SE AMSE A 1 35.685 29.542 -12.339 0.38 37.22 SE ANISOU 13 SE AMSE A 1 4340 4958 4843 19 -66 -968 SE HETATM 14 SE BMSE A 1 38.761 31.763 -16.156 0.37 33.40 SE ANISOU 14 SE BMSE A 1 3930 4805 3953 9 -7 -1049 SE HETATM 15 CE AMSE A 1 33.759 29.349 -12.242 0.50 34.89 C ANISOU 15 CE AMSE A 1 4021 4656 4578 16 -109 -974 C HETATM 16 CE BMSE A 1 40.471 32.273 -15.384 0.50 29.57 C ANISOU 16 CE BMSE A 1 3473 4270 3490 15 39 -974 C