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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
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