HEADER HYDROLASE 16-APR-04 1VK2 TITLE CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE (TM0511) FROM THERMOTOGA TITLE 2 MARITIMA AT 1.90 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE TM0511; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM0511; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TM0511, URACIL-DNA GLYCOSYLASE, STRUCTURAL GENOMICS, JCSG, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 9 13-NOV-24 1VK2 1 REMARK REVDAT 8 25-JAN-23 1VK2 1 REMARK SEQADV LINK REVDAT 7 13-JUL-11 1VK2 1 VERSN REVDAT 6 24-MAR-09 1VK2 1 ATOM CONECT REVDAT 5 24-FEB-09 1VK2 1 VERSN REVDAT 4 28-MAR-06 1VK2 1 JRNL REVDAT 3 18-JAN-05 1VK2 1 AUTHOR KEYWDS REMARK REVDAT 2 03-AUG-04 1VK2 1 TITLE COMPND KEYWDS HEADER REVDAT 1 04-MAY-04 1VK2 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE (TM0511) FROM JRNL TITL 2 THERMOTOGA MARITIMA AT 1.90 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18702 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1013 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1479 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : -2.62000 REMARK 3 B12 (A**2) : 0.00000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.880 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1516 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1427 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2061 ; 1.671 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3303 ; 0.867 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 189 ; 5.693 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 235 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1667 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 300 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 318 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1682 ; 0.239 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 924 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.146 ; 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): 2 ; 0.044 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 31 ; 0.353 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.095 ; 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): 946 ; 2.039 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1539 ; 3.691 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 570 ; 6.419 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 510 ; 9.483 ;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 : 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 201 REMARK 3 ORIGIN FOR THE GROUP (A): 52.7080 21.5221 73.6181 REMARK 3 T TENSOR REMARK 3 T11: 0.0066 T22: 0.0575 REMARK 3 T33: 0.0393 T12: -0.0035 REMARK 3 T13: 0.0035 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.7978 L22: 1.7406 REMARK 3 L33: 2.3389 L12: -0.3729 REMARK 3 L13: -0.9715 L23: 0.0869 REMARK 3 S TENSOR REMARK 3 S11: 0.1389 S12: 0.1117 S13: -0.0024 REMARK 3 S21: -0.0610 S22: -0.0970 S23: 0.1638 REMARK 3 S31: -0.1049 S32: -0.1420 S33: -0.0419 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS AN FE4S4 LIGAND IS COVALENTLY BOUND TO CYS18A, CYS21A, REMARK 3 CYS89A AND CYS105A OF THE PROTEIN. AN UNIDENTIFIED ENTITY AT THE REMARK 3 ACTIVE SITE IS MODELED AS UNL RESIDUE. REMARK 4 REMARK 4 1VK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000001937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000, 0.9796, 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.870 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.13 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.84100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS PH 8.5, 8% PEG-8000, VAPOR REMARK 280 DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K. CRYO REMARK 280 CONDITION: 25% PEG-200. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 63.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.52450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.52450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.52450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.52450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.52450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.52450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.52450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.52450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.87500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.75000 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 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: MONOMERIC 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 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 MET A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 192 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 17 CE NZ REMARK 470 LYS A 54 CD CE NZ REMARK 470 MSE A 65 CE REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 LYS A 142 CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 GLU A 191 CA C O CB CG CD OE1 REMARK 470 GLU A 191 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 ASP A 134 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 167 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -5.8 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 TRP A 150 -165.55 -110.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 AN UNIDENTIFIED ENTITY AT THE ACTIVE SITE IS MODELED AS REMARK 600 A UNL, UNKNOWN LIGAND, RESIDUE. 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 SF4 A 201 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 SF4 A 201 S1 117.9 REMARK 620 3 SF4 A 201 S3 108.6 106.0 REMARK 620 4 SF4 A 201 S4 110.1 105.5 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 SF4 A 201 S1 112.7 REMARK 620 3 SF4 A 201 S2 105.3 105.6 REMARK 620 4 SF4 A 201 S3 120.1 104.9 107.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 89 SG REMARK 620 2 SF4 A 201 S1 120.1 REMARK 620 3 SF4 A 201 S2 105.9 105.4 REMARK 620 4 SF4 A 201 S4 114.9 104.1 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 105 SG REMARK 620 2 SF4 A 201 S2 112.0 REMARK 620 3 SF4 A 201 S3 112.9 105.4 REMARK 620 4 SF4 A 201 S4 115.2 103.2 107.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 282384 RELATED DB: TARGETDB DBREF 1VK2 A 1 192 UNP Q9WYY1 Q9WYY1_THEMA 1 192 SEQADV 1VK2 MET A -11 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 GLY A -10 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 SER A -9 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 ASP A -8 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 LYS A -7 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 ILE A -6 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A -5 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A -4 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A -3 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A -2 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A -1 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 HIS A 0 UNP Q9WYY1 EXPRESSION TAG SEQADV 1VK2 MSE A 1 UNP Q9WYY1 MET 1 MODIFIED RESIDUE SEQADV 1VK2 MSE A 8 UNP Q9WYY1 MET 8 MODIFIED RESIDUE SEQADV 1VK2 MSE A 65 UNP Q9WYY1 MET 65 MODIFIED RESIDUE SEQRES 1 A 204 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 204 TYR THR ARG GLU GLU LEU MSE GLU ILE VAL SER GLU ARG SEQRES 3 A 204 VAL LYS LYS CYS THR ALA CYS PRO LEU HIS LEU ASN ARG SEQRES 4 A 204 THR ASN VAL VAL VAL GLY GLU GLY ASN LEU ASP THR ARG SEQRES 5 A 204 ILE VAL PHE VAL GLY GLU GLY PRO GLY GLU GLU GLU ASP SEQRES 6 A 204 LYS THR GLY ARG PRO PHE VAL GLY ARG ALA GLY MSE LEU SEQRES 7 A 204 LEU THR GLU LEU LEU ARG GLU SER GLY ILE ARG ARG GLU SEQRES 8 A 204 ASP VAL TYR ILE CYS ASN VAL VAL LYS CYS ARG PRO PRO SEQRES 9 A 204 ASN ASN ARG THR PRO THR PRO GLU GLU GLN ALA ALA CYS SEQRES 10 A 204 GLY HIS PHE LEU LEU ALA GLN ILE GLU ILE ILE ASN PRO SEQRES 11 A 204 ASP VAL ILE VAL ALA LEU GLY ALA THR ALA LEU SER PHE SEQRES 12 A 204 PHE VAL ASP GLY LYS LYS VAL SER ILE THR LYS VAL ARG SEQRES 13 A 204 GLY ASN PRO ILE ASP TRP LEU GLY GLY LYS LYS VAL ILE SEQRES 14 A 204 PRO THR PHE HIS PRO SER TYR LEU LEU ARG ASN ARG SER SEQRES 15 A 204 ASN GLU LEU ARG ARG ILE VAL LEU GLU ASP ILE GLU LYS SEQRES 16 A 204 ALA LYS SER PHE ILE LYS LYS GLU GLY MODRES 1VK2 MSE A 1 MET SELENOMETHIONINE MODRES 1VK2 MSE A 8 MET SELENOMETHIONINE MODRES 1VK2 MSE A 65 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 8 8 HET MSE A 65 7 HET SF4 A 201 8 HET UNL A 301 3 HETNAM MSE SELENOMETHIONINE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM UNL UNKNOWN LIGAND FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 SF4 FE4 S4 FORMUL 4 HOH *114(H2 O) HELIX 1 1 THR A 3 CYS A 18 1 16 HELIX 2 2 CYS A 21 ASN A 26 5 6 HELIX 3 3 GLY A 49 GLY A 56 1 8 HELIX 4 4 GLY A 61 SER A 74 1 14 HELIX 5 5 ARG A 77 ASP A 80 5 4 HELIX 6 6 PRO A 91 ARG A 95 5 5 HELIX 7 7 THR A 98 ASN A 117 1 20 HELIX 8 8 GLY A 125 PHE A 132 1 8 HELIX 9 9 SER A 139 ARG A 144 1 6 HELIX 10 10 LEU A 151 GLY A 153 5 3 HELIX 11 11 HIS A 161 ASN A 168 1 8 HELIX 12 12 SER A 170 SER A 186 1 17 SHEET 1 A 6 GLU A 34 GLY A 35 0 SHEET 2 A 6 TYR A 82 ASN A 85 -1 O ILE A 83 N GLU A 34 SHEET 3 A 6 ILE A 41 GLY A 45 1 N PHE A 43 O TYR A 82 SHEET 4 A 6 VAL A 120 LEU A 124 1 O LEU A 124 N VAL A 44 SHEET 5 A 6 LYS A 155 THR A 159 1 O THR A 159 N ALA A 123 SHEET 6 A 6 ILE A 148 ASP A 149 -1 N ILE A 148 O VAL A 156 LINK C MSE A 1 N TYR A 2 1555 1555 1.33 LINK C LEU A 7 N MSE A 8 1555 1555 1.32 LINK C MSE A 8 N GLU A 9 1555 1555 1.33 LINK C GLY A 64 N MSE A 65 1555 1555 1.32 LINK C MSE A 65 N LEU A 66 1555 1555 1.32 LINK SG CYS A 18 FE2 SF4 A 201 1555 1555 2.40 LINK SG CYS A 21 FE4 SF4 A 201 1555 1555 2.26 LINK SG CYS A 89 FE3 SF4 A 201 1555 1555 2.34 LINK SG CYS A 105 FE1 SF4 A 201 1555 1555 2.23 SITE 1 AC1 5 CYS A 18 CYS A 21 HIS A 24 CYS A 89 SITE 2 AC1 5 CYS A 105 SITE 1 AC2 5 GLU A 46 GLY A 47 HIS A 161 HOH A 305 SITE 2 AC2 5 HOH A 319 CRYST1 61.049 61.049 127.500 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016380 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007843 0.00000 HETATM 1 N MSE A 1 52.348 15.410 101.901 1.00 52.89 N HETATM 2 CA MSE A 1 51.657 14.261 101.204 1.00 54.98 C HETATM 3 C MSE A 1 52.261 13.901 99.840 1.00 52.37 C HETATM 4 O MSE A 1 52.931 12.867 99.707 1.00 51.83 O HETATM 5 CB MSE A 1 50.180 14.569 101.009 1.00 56.37 C HETATM 6 CG MSE A 1 49.428 14.568 102.306 1.00 71.15 C HETATM 7 SE MSE A 1 48.472 12.868 102.717 1.00 88.99 SE HETATM 8 CE MSE A 1 46.588 13.785 102.813 1.00 77.31 C