HEADER TRANSFERASE 24-DEC-14 4RZU OBSLTE 01-FEB-23 4RZU 5H70 TITLE CRYSTAL STRUCTURE OF ADP BOUND DTMP KINASE (ST1543) FROM SULFOLOBUS TITLE 2 TOKODAII STRAIN7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE THYMIDYLATE KINASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: DTMP KINASE; COMPND 5 EC: 2.7.4.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TOKODAII; SOURCE 3 ORGANISM_TAXID: 273063; SOURCE 4 STRAIN: STRAIN7; SOURCE 5 GENE: STK_15430, TMK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BISWAS,J.JEYAKANTHAN,K.SEKAR,S.KURAMITSU,S.YOKOYAMA REVDAT 2 01-FEB-23 4RZU 1 OBSLTE REMARK LINK REVDAT 1 30-DEC-15 4RZU 0 JRNL AUTH A.BISWAS,J.JEYAKANTHAN,K.SEKAR,S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF ADP BOUND DTMP KINASE (ST1543) FROM JRNL TITL 2 SULFOLOBUS TOKODAII STRAIN7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10936 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 579 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 780 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3099 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.24000 REMARK 3 B22 (A**2) : -4.68000 REMARK 3 B33 (A**2) : -0.56000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.461 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.386 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.543 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3268 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2938 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4466 ; 1.446 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6709 ; 0.813 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 6.206 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;36.453 ;22.713 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 466 ;15.775 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.076 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 510 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3672 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 748 ; 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): 1651 ; 2.031 ; 3.637 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1650 ; 2.022 ; 3.635 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2060 ; 3.379 ; 5.445 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1966 ; 4.557 ; 5.579 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1617 ; 2.601 ; 3.882 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1542 ; 2.973 ; 3.941 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2302 ; 4.439 ; 5.843 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3778 ; 7.979 ;31.320 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3779 ; 7.978 ;31.336 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 209 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2818 2.6342 2.7149 REMARK 3 T TENSOR REMARK 3 T11: 0.3248 T22: 0.2489 REMARK 3 T33: 0.1876 T12: 0.0227 REMARK 3 T13: -0.0059 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.3695 L22: 1.3397 REMARK 3 L33: 1.4326 L12: 0.2273 REMARK 3 L13: -0.3463 L23: 1.0510 REMARK 3 S TENSOR REMARK 3 S11: -0.1427 S12: 0.0530 S13: -0.0670 REMARK 3 S21: 0.0138 S22: 0.0479 S23: 0.1339 REMARK 3 S31: -0.2118 S32: -0.0370 S33: 0.0948 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 : A 4 A 209 REMARK 3 ORIGIN FOR THE GROUP (A): 33.0358 -9.1090 -24.7991 REMARK 3 T TENSOR REMARK 3 T11: 0.2001 T22: 0.6254 REMARK 3 T33: 0.3935 T12: -0.1706 REMARK 3 T13: 0.1788 T23: -0.4280 REMARK 3 L TENSOR REMARK 3 L11: 2.8480 L22: 2.6901 REMARK 3 L33: 2.2193 L12: 1.3816 REMARK 3 L13: -0.6248 L23: 1.7312 REMARK 3 S TENSOR REMARK 3 S11: -0.4290 S12: 0.7852 S13: -0.3639 REMARK 3 S21: -0.2730 S22: 0.9515 S23: -0.6905 REMARK 3 S31: -0.0588 S32: 0.4412 S33: -0.5224 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4RZU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000088001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : RH COATED BENT-CYRINDRICAL REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 200, 100MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, ADP, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 24.58550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.87900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.89950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.87900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.58550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.89950 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 210 REMARK 465 ASN B 211 REMARK 465 SER B 212 REMARK 465 PHE B 213 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 SER A 41 REMARK 465 ASP A 210 REMARK 465 ASN A 211 REMARK 465 SER A 212 REMARK 465 PHE A 213 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 B 31 CG CD CE NZ REMARK 470 ILE B 48 CG1 CG2 CD1 REMARK 470 LYS B 50 CG CD CE NZ REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 LYS B 55 CG CD CE NZ REMARK 470 ASP B 56 CG OD1 OD2 REMARK 470 LYS B 84 CG CD CE NZ REMARK 470 SER B 85 OG REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 GLU B 137 CG CD OE1 OE2 REMARK 470 LYS B 141 CG CD CE NZ REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 LYS B 145 CG CD CE NZ REMARK 470 LYS B 147 CG CD CE NZ REMARK 470 GLN B 149 CG CD OE1 NE2 REMARK 470 GLU B 162 CG CD OE1 OE2 REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 LYS B 203 CG CD CE NZ REMARK 470 GLU B 207 CG CD OE1 OE2 REMARK 470 LEU B 208 CG CD1 CD2 REMARK 470 ILE B 209 CG1 CG2 CD1 REMARK 470 ILE A 12 CG1 CG2 CD1 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LEU A 30 CG CD1 CD2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 VAL A 34 CG1 CG2 REMARK 470 GLU A 38 CG CD OE1 OE2 REMARK 470 ASN A 40 CG OD1 ND2 REMARK 470 SER A 42 OG REMARK 470 ASP A 43 CG OD1 OD2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 ILE A 90 CG1 CG2 CD1 REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 ILE A 124 CG1 CG2 CD1 REMARK 470 ASP A 133 CG OD1 OD2 REMARK 470 ILE A 134 CG1 CG2 CD1 REMARK 470 LEU A 136 CG CD1 CD2 REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 ILE A 139 CG1 CG2 CD1 REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 SER A 142 OG REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 ILE A 146 CG1 CG2 CD1 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 GLN A 149 CG CD OE1 NE2 REMARK 470 ILE A 155 CG1 CG2 CD1 REMARK 470 GLU A 162 CG CD OE1 OE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 PHE A 165 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 166 CG CD1 CD2 REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 VAL A 187 CG1 CG2 REMARK 470 ILE A 188 CG1 CG2 CD1 REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 GLU A 196 CG CD OE1 OE2 REMARK 470 ILE A 197 CG1 CG2 CD1 REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 ILE A 201 CG1 CG2 CD1 REMARK 470 LYS A 203 CG CD CE NZ REMARK 470 PHE A 204 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 ILE A 209 CG1 CG2 CD1 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 LYS B 50 -70.66 -56.51 REMARK 500 LYS B 53 2.77 -62.28 REMARK 500 LYS B 54 -67.08 -104.16 REMARK 500 ILE B 79 -70.45 -62.90 REMARK 500 ARG B 93 156.94 73.79 REMARK 500 ARG B 93 159.67 68.61 REMARK 500 TYR B 94 -161.77 -168.87 REMARK 500 LYS B 147 135.79 -37.28 REMARK 500 PHE B 156 71.12 -115.12 REMARK 500 LYS B 192 -169.37 -67.13 REMARK 500 ILE A 12 174.34 -48.89 REMARK 500 ASP A 43 163.99 -42.39 REMARK 500 TRP A 44 -42.43 -29.84 REMARK 500 TYR A 78 -66.68 -94.98 REMARK 500 PHE A 87 156.58 -38.77 REMARK 500 ARG A 93 130.85 85.60 REMARK 500 ARG A 93 130.81 85.50 REMARK 500 TYR A 94 -152.04 -133.15 REMARK 500 ASP A 108 108.72 -41.27 REMARK 500 PRO A 122 164.05 -45.28 REMARK 500 LYS A 143 8.39 87.58 REMARK 500 LEU A 208 -63.15 -24.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 18 OG REMARK 620 2 ADP B 301 O3B 69.7 REMARK 620 3 HOH B 401 O 70.7 52.5 REMARK 620 4 HOH B 402 O 128.4 61.8 66.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 18 OG REMARK 620 2 ADP A 301 O1B 59.3 REMARK 620 3 ADP A 301 O3A 74.1 56.2 REMARK 620 4 HOH A 404 O 117.2 124.3 167.9 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 ADP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PLR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DTMP KINASE (ST1543) FROM SULFOLOBUS TOKODAII REMARK 900 STRAIN7 REMARK 900 RELATED ID: 4NZY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE (TYPE-2) OF DTMP KINASE (ST1543) FROM SULFOLOBUS REMARK 900 TOKODAII STRAIN7 REMARK 900 RELATED ID: 4RZX RELATED DB: PDB DBREF 4RZU B 1 213 UNP Q970Q8 KTHY2_SULTO 1 213 DBREF 4RZU A 1 213 UNP Q970Q8 KTHY2_SULTO 1 213 SEQRES 1 B 213 MET LYS LYS GLY VAL LEU ILE ALA PHE GLU GLY ILE ASP SEQRES 2 B 213 GLY SER GLY LYS SER SER GLN ALA THR LEU LEU LYS ASP SEQRES 3 B 213 TRP ILE GLU LEU LYS ARG ASP VAL TYR LEU THR GLU TRP SEQRES 4 B 213 ASN SER SER ASP TRP ILE HIS ASP ILE ILE LYS GLU ALA SEQRES 5 B 213 LYS LYS LYS ASP LEU LEU THR PRO LEU THR PHE SER LEU SEQRES 6 B 213 ILE HIS ALA THR ASP PHE SER ASP ARG TYR GLU ARG TYR SEQRES 7 B 213 ILE LEU PRO MET LEU LYS SER GLY PHE ILE VAL ILE SER SEQRES 8 B 213 ASP ARG TYR ILE TYR THR ALA TYR ALA ARG ASP SER VAL SEQRES 9 B 213 ARG GLY VAL ASP ILE ASP TRP VAL LYS LYS LEU TYR SER SEQRES 10 B 213 PHE ALA ILE LYS PRO ASP ILE THR PHE TYR ILE ARG VAL SEQRES 11 B 213 SER PRO ASP ILE ALA LEU GLU ARG ILE LYS LYS SER LYS SEQRES 12 B 213 ARG LYS ILE LYS PRO GLN GLU ALA GLY ALA ASP ILE PHE SEQRES 13 B 213 PRO GLY LEU SER PRO GLU GLU GLY PHE LEU LYS TYR GLN SEQRES 14 B 213 GLY LEU ILE THR GLU VAL TYR ASP LYS LEU VAL LYS ASP SEQRES 15 B 213 GLU ASN PHE ILE VAL ILE ASP GLY THR LYS THR PRO LYS SEQRES 16 B 213 GLU ILE GLN ILE GLN ILE ARG LYS PHE VAL GLY GLU LEU SEQRES 17 B 213 ILE ASP ASN SER PHE SEQRES 1 A 213 MET LYS LYS GLY VAL LEU ILE ALA PHE GLU GLY ILE ASP SEQRES 2 A 213 GLY SER GLY LYS SER SER GLN ALA THR LEU LEU LYS ASP SEQRES 3 A 213 TRP ILE GLU LEU LYS ARG ASP VAL TYR LEU THR GLU TRP SEQRES 4 A 213 ASN SER SER ASP TRP ILE HIS ASP ILE ILE LYS GLU ALA SEQRES 5 A 213 LYS LYS LYS ASP LEU LEU THR PRO LEU THR PHE SER LEU SEQRES 6 A 213 ILE HIS ALA THR ASP PHE SER ASP ARG TYR GLU ARG TYR SEQRES 7 A 213 ILE LEU PRO MET LEU LYS SER GLY PHE ILE VAL ILE SER SEQRES 8 A 213 ASP ARG TYR ILE TYR THR ALA TYR ALA ARG ASP SER VAL SEQRES 9 A 213 ARG GLY VAL ASP ILE ASP TRP VAL LYS LYS LEU TYR SER SEQRES 10 A 213 PHE ALA ILE LYS PRO ASP ILE THR PHE TYR ILE ARG VAL SEQRES 11 A 213 SER PRO ASP ILE ALA LEU GLU ARG ILE LYS LYS SER LYS SEQRES 12 A 213 ARG LYS ILE LYS PRO GLN GLU ALA GLY ALA ASP ILE PHE SEQRES 13 A 213 PRO GLY LEU SER PRO GLU GLU GLY PHE LEU LYS TYR GLN SEQRES 14 A 213 GLY LEU ILE THR GLU VAL TYR ASP LYS LEU VAL LYS ASP SEQRES 15 A 213 GLU ASN PHE ILE VAL ILE ASP GLY THR LYS THR PRO LYS SEQRES 16 A 213 GLU ILE GLN ILE GLN ILE ARG LYS PHE VAL GLY GLU LEU SEQRES 17 A 213 ILE ASP ASN SER PHE HET ADP B 301 27 HET EDO B 302 4 HET MG B 303 1 HET ADP A 301 27 HET EDO A 302 4 HET PGE A 303 10 HET MG A 304 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 5 MG 2(MG 2+) FORMUL 8 PGE C6 H14 O4 FORMUL 10 HOH *6(H2 O) HELIX 1 1 GLY B 16 GLU B 29 1 14 HELIX 2 2 SER B 42 ASP B 56 1 15 HELIX 3 3 THR B 59 TYR B 78 1 20 HELIX 4 4 TYR B 78 SER B 85 1 8 HELIX 5 5 TYR B 94 VAL B 104 1 11 HELIX 6 6 ASP B 108 SER B 117 1 10 HELIX 7 7 SER B 131 SER B 142 1 12 HELIX 8 8 LYS B 147 ALA B 151 5 5 HELIX 9 9 SER B 160 ASN B 184 1 25 HELIX 10 10 THR B 193 ILE B 209 1 17 HELIX 11 11 GLY A 16 ARG A 32 1 17 HELIX 12 12 ASP A 43 LYS A 53 1 11 HELIX 13 13 THR A 59 TYR A 78 1 20 HELIX 14 14 TYR A 78 GLY A 86 1 9 HELIX 15 15 TYR A 94 VAL A 104 1 11 HELIX 16 16 ASP A 108 TYR A 116 1 9 HELIX 17 17 SER A 131 SER A 142 1 12 HELIX 18 18 LYS A 147 GLY A 152 1 6 HELIX 19 19 SER A 160 ASN A 184 1 25 HELIX 20 20 THR A 193 GLU A 207 1 15 SHEET 1 A 5 VAL B 34 GLU B 38 0 SHEET 2 A 5 ILE B 88 ASP B 92 1 O ILE B 90 N THR B 37 SHEET 3 A 5 VAL B 5 GLU B 10 1 N VAL B 5 O VAL B 89 SHEET 4 A 5 ILE B 124 ARG B 129 1 O PHE B 126 N ALA B 8 SHEET 5 A 5 PHE B 185 ASP B 189 1 O ILE B 186 N TYR B 127 SHEET 1 B 5 VAL A 34 GLU A 38 0 SHEET 2 B 5 ILE A 88 ASP A 92 1 O ASP A 92 N THR A 37 SHEET 3 B 5 VAL A 5 GLU A 10 1 N ILE A 7 O VAL A 89 SHEET 4 B 5 ILE A 124 ARG A 129 1 O ILE A 128 N GLU A 10 SHEET 5 B 5 ILE A 186 ASP A 189 1 O ILE A 188 N ARG A 129 LINK OG SER B 18 MG MG B 303 1555 1555 1.97 LINK O3B ADP B 301 MG MG B 303 1555 1555 2.66 LINK MG MG B 303 O HOH B 401 1555 1555 2.71 LINK MG MG B 303 O HOH B 402 1555 1555 2.26 LINK OG SER A 18 MG MG A 304 1555 1555 2.41 LINK O1B ADP A 301 MG MG A 304 1555 1555 2.45 LINK O3A ADP A 301 MG MG A 304 1555 1555 2.77 LINK MG MG A 304 O HOH A 404 1555 1555 2.89 SITE 1 AC1 13 GLY B 14 SER B 15 GLY B 16 LYS B 17 SITE 2 AC1 13 SER B 18 SER B 19 ARG B 138 LYS B 192 SITE 3 AC1 13 PRO B 194 ILE B 197 MG B 303 HOH B 401 SITE 4 AC1 13 HOH B 402 SITE 1 AC2 2 PHE A 118 TRP B 111 SITE 1 AC3 5 SER B 18 ASP B 92 ADP B 301 HOH B 401 SITE 2 AC3 5 HOH B 402 SITE 1 AC4 12 ASP A 13 GLY A 14 SER A 15 GLY A 16 SITE 2 AC4 12 LYS A 17 SER A 18 SER A 19 ARG A 138 SITE 3 AC4 12 SER A 142 LYS A 192 PRO A 194 MG A 304 SITE 1 AC5 4 PHE A 63 ARG A 105 ASP A 154 PGE A 303 SITE 1 AC6 3 HIS A 46 ASP A 154 EDO A 302 SITE 1 AC7 3 SER A 18 ADP A 301 HOH A 404 CRYST1 49.171 63.799 141.758 90.00 90.00 90.00 P 21 21 21 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 0.020337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007054 0.00000