PDB Short entry for 1VK8 HEADER BIOSYNTHETIC PROTEIN 05-MAY-04 1VK8 TITLE CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN TITLE 2 (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN TM0486; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM0486; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 25-JAN-23 1VK8 1 REMARK SEQADV LINK REVDAT 7 13-JUL-11 1VK8 1 VERSN REVDAT 6 28-JUL-10 1VK8 1 HEADER JRNL KEYWDS TITLE REVDAT 5 24-FEB-09 1VK8 1 VERSN REVDAT 4 28-MAR-06 1VK8 1 JRNL REVDAT 3 18-JAN-05 1VK8 1 AUTHOR KEYWDS REMARK REVDAT 2 10-AUG-04 1VK8 1 JRNL TITLE COMPND KEYWDS REVDAT 1 18-MAY-04 1VK8 0 JRNL AUTH Z.DERMOUN,A.FOULON,M.D.MILLER,D.J.HARRINGTON,A.M.DEACON, JRNL AUTH 2 C.SEBBAN-KREUZER,P.ROCHE,D.LAFITTE,O.BORNET,I.A.WILSON, JRNL AUTH 3 A.DOLLA JRNL TITL TM0486 FROM THE HYPERTHERMOPHILIC ANAEROBE THERMOTOGA JRNL TITL 2 MARITIMA IS A THIAMIN-BINDING PROTEIN INVOLVED IN RESPONSE JRNL TITL 3 OF THE CELL TO OXIDATIVE CONDITIONS. JRNL REF J.MOL.BIOL. V. 400 463 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20471400 JRNL DOI 10.1016/J.JMB.2010.05.014 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 76.1 REMARK 3 NUMBER OF REFLECTIONS : 24544 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) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1336 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) : 574 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 353 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -1.19000 REMARK 3 B12 (A**2) : 0.52000 REMARK 3 B13 (A**2) : 0.44000 REMARK 3 B23 (A**2) : -0.03000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.867 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3085 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2905 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4142 ; 1.443 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6768 ; 1.047 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 369 ; 5.811 ; 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): 462 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3344 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 618 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 739 ; 0.397 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3518 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1973 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 288 ; 0.192 ; 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): 7 ; 0.136 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.220 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.193 ; 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): 1854 ; 1.737 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3015 ; 3.301 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1231 ; 5.719 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1127 ; 8.941 ;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 : 4 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 94 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2120 15.3340 38.5290 REMARK 3 T TENSOR REMARK 3 T11: 0.0261 T22: 0.0211 REMARK 3 T33: 0.0095 T12: 0.0034 REMARK 3 T13: -0.0065 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.0718 L22: 1.9619 REMARK 3 L33: 0.9700 L12: 0.5391 REMARK 3 L13: -0.3286 L23: -0.1567 REMARK 3 S TENSOR REMARK 3 S11: -0.0253 S12: 0.0908 S13: -0.0445 REMARK 3 S21: -0.0511 S22: 0.0484 S23: 0.0688 REMARK 3 S31: 0.0392 S32: -0.0348 S33: -0.0232 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 2 B 94 REMARK 3 ORIGIN FOR THE GROUP (A): 34.7190 25.4110 45.7740 REMARK 3 T TENSOR REMARK 3 T11: 0.0240 T22: 0.0287 REMARK 3 T33: 0.0066 T12: 0.0096 REMARK 3 T13: -0.0125 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 2.1409 L22: 1.0041 REMARK 3 L33: 0.8099 L12: 0.4341 REMARK 3 L13: -0.3757 L23: -0.2202 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: -0.0176 S13: 0.0129 REMARK 3 S21: 0.0865 S22: -0.0375 S23: -0.0809 REMARK 3 S31: -0.0343 S32: 0.0415 S33: -0.0248 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 94 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0240 30.2710 45.6400 REMARK 3 T TENSOR REMARK 3 T11: 0.0302 T22: 0.0311 REMARK 3 T33: 0.0288 T12: 0.0042 REMARK 3 T13: 0.0207 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 2.2123 L22: 1.4198 REMARK 3 L33: 0.8047 L12: 0.6943 REMARK 3 L13: 0.5713 L23: 0.8653 REMARK 3 S TENSOR REMARK 3 S11: 0.0784 S12: -0.0704 S13: 0.0461 REMARK 3 S21: 0.1400 S22: -0.0801 S23: 0.1508 REMARK 3 S31: 0.1066 S32: -0.0579 S33: 0.0017 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 94 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6480 40.3190 38.4330 REMARK 3 T TENSOR REMARK 3 T11: 0.0195 T22: 0.0290 REMARK 3 T33: 0.0209 T12: 0.0032 REMARK 3 T13: 0.0020 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.3222 L22: 2.0776 REMARK 3 L33: 0.7350 L12: 0.8407 REMARK 3 L13: 0.6228 L23: 0.6055 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: 0.1328 S13: 0.0830 REMARK 3 S21: -0.0087 S22: 0.0318 S23: 0.0253 REMARK 3 S31: -0.0478 S32: 0.0529 S33: -0.0123 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: REMARK 3 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 REMARK 3 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF REMARK 3 THIS MOIETY WAS NOT POSSIBLE, THOUGH THE DENSITY REMARK 3 CAN BE CLOSELY ACCOUNTED FOR BY A GUANINE BASE. IT IS REMARK 3 LABELED 'UNL' AND ALL ATOMS WERE REFINED AS OXYGEN REMARK 3 ATOMS. BUMP RESTRAINTS WERE REMOVED FOR THE REFINEMENT REMARK 3 OF ATOMS IN EACH OF THESE LIGANDS. REMARK 3 3). TLS GROUPS WERE CHOSEN BY PROTEIN SUBUNIT IDENTIFICATION REMARK 3 IN THE CRYSTALLOGRAPHIC ASSYMETRIC UNIT. REMARK 4 REMARK 4 1VK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000001942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.6 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) : 1.0332, 0.9796 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25897 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 23.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-8000, 0.1M CHES PH 9.5, PH REMARK 280 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K. REMARK 280 CRYO CONDITION: 12% PEG 200. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MSE A 1 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MSE B 1 REMARK 465 MET C -11 REMARK 465 GLY C -10 REMARK 465 SER C -9 REMARK 465 ASP C -8 REMARK 465 LYS C -7 REMARK 465 ILE C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 HIS C -1 REMARK 465 HIS C 0 REMARK 465 MET D -11 REMARK 465 GLY D -10 REMARK 465 SER D -9 REMARK 465 ASP D -8 REMARK 465 LYS D -7 REMARK 465 ILE D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 HIS D -1 REMARK 465 HIS D 0 REMARK 465 MSE D 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MSE C 1 SE CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 93 OD1 ASP C 24 1.98 REMARK 500 N PRO D 2 O HOH D 451 2.07 REMARK 500 OH TYR A 79 OE2 GLU B 65 2.08 REMARK 500 OD1 ASP B 24 OH TYR D 93 2.18 REMARK 500 OD1 ASP A 24 OH TYR C 93 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 16 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP B 76 CB - CG - OD2 ANGL. DEV. = 5.4 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 ASP C 16 -39.98 -39.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL C 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL D 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 282359 RELATED DB: TARGETDB DBREF 1VK8 A 1 94 UNP Q9WYV6 Q9WYV6_THEMA 1 94 DBREF 1VK8 B 1 94 UNP Q9WYV6 Q9WYV6_THEMA 1 94 DBREF 1VK8 C 1 94 UNP Q9WYV6 Q9WYV6_THEMA 1 94 DBREF 1VK8 D 1 94 UNP Q9WYV6 Q9WYV6_THEMA 1 94 SEQADV 1VK8 MET A -11 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 GLY A -10 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 SER A -9 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ASP A -8 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 LYS A -7 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ILE A -6 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A -5 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A -4 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A -3 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A -2 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A -1 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS A 0 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 MSE A 1 UNP Q9WYV6 MET 1 MODIFIED RESIDUE SEQADV 1VK8 MSE A 35 UNP Q9WYV6 MET 35 MODIFIED RESIDUE SEQADV 1VK8 MSE A 54 UNP Q9WYV6 MET 54 MODIFIED RESIDUE SEQADV 1VK8 MET B -11 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 GLY B -10 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 SER B -9 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ASP B -8 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 LYS B -7 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ILE B -6 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B -5 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B -4 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B -3 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B -2 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B -1 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS B 0 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 MSE B 1 UNP Q9WYV6 MET 1 MODIFIED RESIDUE SEQADV 1VK8 MSE B 35 UNP Q9WYV6 MET 35 MODIFIED RESIDUE SEQADV 1VK8 MSE B 54 UNP Q9WYV6 MET 54 MODIFIED RESIDUE SEQADV 1VK8 MET C -11 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 GLY C -10 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 SER C -9 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ASP C -8 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 LYS C -7 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ILE C -6 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C -5 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C -4 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C -3 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C -2 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C -1 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS C 0 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 MSE C 1 UNP Q9WYV6 MET 1 MODIFIED RESIDUE SEQADV 1VK8 MSE C 35 UNP Q9WYV6 MET 35 MODIFIED RESIDUE SEQADV 1VK8 MSE C 54 UNP Q9WYV6 MET 54 MODIFIED RESIDUE SEQADV 1VK8 MET D -11 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 GLY D -10 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 SER D -9 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ASP D -8 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 LYS D -7 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 ILE D -6 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D -5 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D -4 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D -3 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D -2 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D -1 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 HIS D 0 UNP Q9WYV6 EXPRESSION TAG SEQADV 1VK8 MSE D 1 UNP Q9WYV6 MET 1 MODIFIED RESIDUE SEQADV 1VK8 MSE D 35 UNP Q9WYV6 MET 35 MODIFIED RESIDUE SEQADV 1VK8 MSE D 54 UNP Q9WYV6 MET 54 MODIFIED RESIDUE SEQRES 1 A 106 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 106 PRO LYS VAL THR VAL SER ILE LYS VAL VAL PRO ALA VAL SEQRES 3 A 106 GLU ASP GLY ARG LEU HIS GLU VAL ILE ASP ARG ALA ILE SEQRES 4 A 106 GLU LYS ILE SER SER TRP GLY MSE LYS TYR GLU VAL GLY SEQRES 5 A 106 PRO SER ASN THR THR VAL GLU GLY GLU PHE GLU GLU ILE SEQRES 6 A 106 MSE ASP ARG VAL LYS GLU LEU ALA ARG TYR LEU GLU GLN SEQRES 7 A 106 PHE ALA LYS ARG PHE VAL LEU GLN LEU ASP ILE ASP TYR SEQRES 8 A 106 LYS ALA GLY GLY ILE THR ILE GLU GLU LYS VAL SER LYS SEQRES 9 A 106 TYR ARG SEQRES 1 B 106 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 B 106 PRO LYS VAL THR VAL SER ILE LYS VAL VAL PRO ALA VAL SEQRES 3 B 106 GLU ASP GLY ARG LEU HIS GLU VAL ILE ASP ARG ALA ILE SEQRES 4 B 106 GLU LYS ILE SER SER TRP GLY MSE LYS TYR GLU VAL GLY SEQRES 5 B 106 PRO SER ASN THR THR VAL GLU GLY GLU PHE GLU GLU ILE SEQRES 6 B 106 MSE ASP ARG VAL LYS GLU LEU ALA ARG TYR LEU GLU GLN SEQRES 7 B 106 PHE ALA LYS ARG PHE VAL LEU GLN LEU ASP ILE ASP TYR SEQRES 8 B 106 LYS ALA GLY GLY ILE THR ILE GLU GLU LYS VAL SER LYS SEQRES 9 B 106 TYR ARG SEQRES 1 C 106 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 C 106 PRO LYS VAL THR VAL SER ILE LYS VAL VAL PRO ALA VAL SEQRES 3 C 106 GLU ASP GLY ARG LEU HIS GLU VAL ILE ASP ARG ALA ILE SEQRES 4 C 106 GLU LYS ILE SER SER TRP GLY MSE LYS TYR GLU VAL GLY SEQRES 5 C 106 PRO SER ASN THR THR VAL GLU GLY GLU PHE GLU GLU ILE SEQRES 6 C 106 MSE ASP ARG VAL LYS GLU LEU ALA ARG TYR LEU GLU GLN SEQRES 7 C 106 PHE ALA LYS ARG PHE VAL LEU GLN LEU ASP ILE ASP TYR SEQRES 8 C 106 LYS ALA GLY GLY ILE THR ILE GLU GLU LYS VAL SER LYS SEQRES 9 C 106 TYR ARG SEQRES 1 D 106 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 D 106 PRO LYS VAL THR VAL SER ILE LYS VAL VAL PRO ALA VAL SEQRES 3 D 106 GLU ASP GLY ARG LEU HIS GLU VAL ILE ASP ARG ALA ILE SEQRES 4 D 106 GLU LYS ILE SER SER TRP GLY MSE LYS TYR GLU VAL GLY SEQRES 5 D 106 PRO SER ASN THR THR VAL GLU GLY GLU PHE GLU GLU ILE SEQRES 6 D 106 MSE ASP ARG VAL LYS GLU LEU ALA ARG TYR LEU GLU GLN SEQRES 7 D 106 PHE ALA LYS ARG PHE VAL LEU GLN LEU ASP ILE ASP TYR SEQRES 8 D 106 LYS ALA GLY GLY ILE THR ILE GLU GLU LYS VAL SER LYS SEQRES 9 D 106 TYR ARG MODRES 1VK8 MSE A 35 MET SELENOMETHIONINE MODRES 1VK8 MSE A 54 MET SELENOMETHIONINE MODRES 1VK8 MSE B 35 MET SELENOMETHIONINE MODRES 1VK8 MSE B 54 MET SELENOMETHIONINE MODRES 1VK8 MSE C 1 MET SELENOMETHIONINE MODRES 1VK8 MSE C 35 MET SELENOMETHIONINE MODRES 1VK8 MSE C 54 MET SELENOMETHIONINE MODRES 1VK8 MSE D 35 MET SELENOMETHIONINE MODRES 1VK8 MSE D 54 MET SELENOMETHIONINE HET MSE A 35 8 HET MSE A 54 8 HET MSE B 35 8 HET MSE B 54 8 HET MSE C 1 6 HET MSE C 35 8 HET MSE C 54 8 HET MSE D 35 8 HET MSE D 54 8 HET UNL A 400 12 HET UNL B 400 12 HET UNL C 400 12 HET UNL D 400 12 HETNAM MSE SELENOMETHIONINE HETNAM UNL UNKNOWN LIGAND FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 9 HOH *353(H2 O) HELIX 1 1 GLU A 15 GLY A 17 5 3 HELIX 2 2 ARG A 18 SER A 32 1 15 HELIX 3 3 GLU A 49 GLU A 65 1 17 HELIX 4 4 THR A 85 SER A 91 1 7 HELIX 5 5 LYS A 92 ARG A 94 5 3 HELIX 6 6 GLU B 15 SER B 32 1 18 HELIX 7 7 PHE B 50 GLU B 65 1 16 HELIX 8 8 THR B 85 SER B 91 1 7 HELIX 9 9 LYS B 92 ARG B 94 5 3 HELIX 10 10 GLU C 15 GLY C 17 5 3 HELIX 11 11 ARG C 18 SER C 32 1 15 HELIX 12 12 GLU C 49 GLU C 65 1 17 HELIX 13 13 THR C 85 SER C 91 1 7 HELIX 14 14 LYS C 92 ARG C 94 5 3 HELIX 15 15 GLU D 15 GLY D 17 5 3 HELIX 16 16 ARG D 18 SER D 32 1 15 HELIX 17 17 GLU D 49 GLU D 65 1 17 HELIX 18 18 THR D 85 SER D 91 1 7 HELIX 19 19 LYS D 92 ARG D 94 5 3 SHEET 1 A 8 TYR A 37 VAL A 39 0 SHEET 2 A 8 THR A 44 GLY A 48 -1 O THR A 45 N GLU A 38 SHEET 3 A 8 VAL A 4 PRO A 12 -1 N ILE A 8 O THR A 44 SHEET 4 A 8 ARG A 70 LYS A 80 -1 O GLN A 74 N LYS A 9 SHEET 5 A 8 ARG B 70 LYS B 80 -1 O ILE B 77 N LEU A 73 SHEET 6 A 8 LYS B 3 PRO B 12 -1 N LYS B 9 O GLN B 74 SHEET 7 A 8 THR B 44 GLU B 49 -1 O THR B 44 N ILE B 8 SHEET 8 A 8 TYR B 37 VAL B 39 -1 N GLU B 38 O THR B 45 SHEET 1 B 8 LYS C 36 VAL C 39 0 SHEET 2 B 8 THR C 44 GLY C 48 -1 O THR C 45 N GLU C 38 SHEET 3 B 8 VAL C 4 PRO C 12 -1 N ILE C 8 O THR C 44 SHEET 4 B 8 ARG C 70 LYS C 80 -1 O VAL C 72 N VAL C 11 SHEET 5 B 8 ARG D 70 LYS D 80 -1 O LEU D 73 N ILE C 77 SHEET 6 B 8 VAL D 4 PRO D 12 -1 N THR D 5 O ASP D 78 SHEET 7 B 8 THR D 44 GLY D 48 -1 O THR D 44 N ILE D 8 SHEET 8 B 8 TYR D 37 VAL D 39 -1 N GLU D 38 O THR D 45 LINK C GLY A 34 N MSE A 35 1555 1555 1.32 LINK C MSE A 35 N LYS A 36 1555 1555 1.34 LINK C ILE A 53 N MSE A 54 1555 1555 1.33 LINK C MSE A 54 N ASP A 55 1555 1555 1.35 LINK C GLY B 34 N MSE B 35 1555 1555 1.32 LINK C MSE B 35 N LYS B 36 1555 1555 1.33 LINK C ILE B 53 N MSE B 54 1555 1555 1.34 LINK C MSE B 54 N ASP B 55 1555 1555 1.33 LINK C MSE C 1 N PRO C 2 1555 1555 1.33 LINK C GLY C 34 N MSE C 35 1555 1555 1.32 LINK C MSE C 35 N LYS C 36 1555 1555 1.33 LINK C ILE C 53 N MSE C 54 1555 1555 1.33 LINK C MSE C 54 N ASP C 55 1555 1555 1.34 LINK C GLY D 34 N MSE D 35 1555 1555 1.33 LINK C MSE D 35 N LYS D 36 1555 1555 1.32 LINK C ILE D 53 N MSE D 54 1555 1555 1.33 LINK C MSE D 54 N ASP D 55 1555 1555 1.35 SITE 1 AC1 12 ILE A 8 LYS A 9 VAL A 10 HIS A 20 SITE 2 AC1 12 ILE A 23 VAL A 39 GLY A 40 PRO A 41 SITE 3 AC1 12 SER A 42 ASN A 43 THR A 44 HOH A 477 SITE 1 AC2 11 ILE B 8 LYS B 9 VAL B 10 HIS B 20 SITE 2 AC2 11 VAL B 39 GLY B 40 PRO B 41 SER B 42 SITE 3 AC2 11 ASN B 43 THR B 44 LYS D 89 SITE 1 AC3 11 LYS A 89 ILE C 8 LYS C 9 VAL C 10 SITE 2 AC3 11 ILE C 23 ILE C 30 VAL C 39 GLY C 40 SITE 3 AC3 11 PRO C 41 ASN C 43 THR C 44 SITE 1 AC4 11 LYS B 89 ILE D 8 LYS D 9 VAL D 10 SITE 2 AC4 11 ILE D 30 VAL D 39 GLY D 40 PRO D 41 SITE 3 AC4 11 SER D 42 ASN D 43 THR D 44 CRYST1 47.646 47.650 49.608 73.80 62.90 73.62 P 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020988 -0.006169 -0.009806 0.00000 SCALE2 0.000000 0.021874 -0.003916 0.00000 SCALE3 0.000000 0.000000 0.023004 0.00000