HEADER TRANSFERASE 06-NOV-16 5H5K TITLE ATP AND CMP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) TITLE 2 FROM AQUIFEX AEOLICUS VF5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DTMP KINASE; COMPND 5 EC: 2.7.4.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS (STRAIN VF5); SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: TMK, AQ_969; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS KINASE, TRANFERASE, COMPLEX, NUCLEOTIDE BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BISWAS,J.JEYAKANTHAN,K.SEKAR REVDAT 3 08-NOV-23 5H5K 1 LINK REVDAT 2 30-AUG-17 5H5K 1 JRNL REVDAT 1 28-JUN-17 5H5K 0 JRNL AUTH A.BISWAS,A.SHUKLA,S.K.CHAUDHARY,R.SANTHOSH,J.JEYAKANTHAN, JRNL AUTH 2 K.SEKAR JRNL TITL STRUCTURAL STUDIES OF A HYPERTHERMOPHILIC THYMIDYLATE KINASE JRNL TITL 2 ENZYME REVEAL CONFORMATIONAL SUBSTATES ALONG THE REACTION JRNL TITL 3 COORDINATE JRNL REF FEBS J. V. 284 2527 2017 JRNL REFN ISSN 1742-4658 JRNL PMID 28627020 JRNL DOI 10.1111/FEBS.14140 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 17588 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 939 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1269 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.94000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.78000 REMARK 3 B13 (A**2) : 2.41000 REMARK 3 B23 (A**2) : 4.65000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.371 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.240 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.395 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3159 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3074 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4275 ; 1.669 ; 2.042 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7058 ; 0.968 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 6.070 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;37.313 ;24.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 570 ;15.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.221 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3399 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 656 ; 0.002 ; 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): 1546 ; 2.508 ; 3.894 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1545 ; 2.508 ; 3.891 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1930 ; 3.773 ; 5.830 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1931 ; 3.772 ; 5.833 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1613 ; 3.115 ; 4.274 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1609 ; 3.108 ; 4.268 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2338 ; 4.645 ; 6.312 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3476 ; 6.071 ;46.165 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3477 ; 6.071 ;46.181 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 195 1 REMARK 3 1 B 1 B 195 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 2911 ; 4.02 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5H5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 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) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18641 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.53200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2PBR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10% W/V POLYETHYLENE REMARK 280 GLYCOL 8000, 8% V/V ETHYLENE GLYCOL, PH 7.5, MICROBATCH, REMARK 280 TEMPERATURE 293.0K 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ARG A 194 REMARK 465 VAL A 195 REMARK 465 ARG B 194 REMARK 465 VAL B 195 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 18 CD CE NZ REMARK 470 LYS A 25 CE NZ REMARK 470 GLN A 26 OE1 NE2 REMARK 470 LYS A 27 CE NZ REMARK 470 LYS A 41 CE NZ REMARK 470 GLU A 48 CD OE1 OE2 REMARK 470 GLU A 54 CD OE1 OE2 REMARK 470 ARG A 82 NE CZ NH1 NH2 REMARK 470 LYS A 122 CE NZ REMARK 470 ASP A 134 OD1 OD2 REMARK 470 ARG A 138 CD NE CZ NH1 NH2 REMARK 470 LYS A 141 CE NZ REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLU A 161 OE1 OE2 REMARK 470 LYS A 164 CE NZ REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 LYS A 183 CE NZ REMARK 470 LYS B 18 CD CE NZ REMARK 470 LYS B 25 CD CE NZ REMARK 470 GLN B 26 CD OE1 NE2 REMARK 470 LYS B 27 CE NZ REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 GLU B 48 CD OE1 OE2 REMARK 470 GLU B 54 CD OE1 OE2 REMARK 470 LYS B 111 NZ REMARK 470 LYS B 122 CE NZ REMARK 470 ASP B 134 CG OD1 OD2 REMARK 470 ARG B 138 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 141 CE NZ REMARK 470 GLU B 142 OE1 OE2 REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 ASN B 144 CG OD1 ND2 REMARK 470 ARG B 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 157 CD CE NZ REMARK 470 GLU B 161 OE1 OE2 REMARK 470 LYS B 164 CD CE NZ REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 GLU B 177 CG CD OE1 OE2 REMARK 470 LYS B 183 NZ REMARK 470 GLU B 184 CD OE1 OE2 REMARK 470 ARG B 187 CG CD NE CZ NH1 NH2 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 O GLU B 166 O HOH B 301 2.18 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 173 CB - CG - OD1 ANGL. DEV. = 6.1 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 LYS A 75 -55.99 -125.23 REMARK 500 ARG A 90 145.80 82.87 REMARK 500 PHE A 91 -141.66 -156.48 REMARK 500 LYS B 75 -54.23 -123.46 REMARK 500 ARG B 90 144.32 81.64 REMARK 500 PHE B 91 -140.20 -154.74 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 A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 ATP A 202 O1G 150.5 REMARK 620 3 ATP A 202 O1B 69.8 82.6 REMARK 620 4 HOH A 308 O 74.6 84.6 64.9 REMARK 620 5 HOH A 314 O 77.1 119.9 136.5 79.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 14 OG1 REMARK 620 2 ATP B 202 O1G 147.8 REMARK 620 3 ATP B 202 O1B 73.0 79.6 REMARK 620 4 C5P B 203 O1P 143.9 68.2 136.2 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 MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5P A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5P B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PBR RELATED DB: PDB REMARK 900 RELATED ID: 5H56 RELATED DB: PDB REMARK 900 RELATED ID: 5H5B RELATED DB: PDB DBREF 5H5K A 1 195 UNP O67099 KTHY_AQUAE 1 195 DBREF 5H5K B 1 195 UNP O67099 KTHY_AQUAE 1 195 SEQRES 1 A 195 MET LEU ILE ALA PHE GLU GLY ILE ASP GLY SER GLY LYS SEQRES 2 A 195 THR THR GLN ALA LYS LYS LEU TYR GLU TYR LEU LYS GLN SEQRES 3 A 195 LYS GLY TYR PHE VAL SER LEU TYR ARG GLU PRO GLY GLY SEQRES 4 A 195 THR LYS VAL GLY GLU VAL LEU ARG GLU ILE LEU LEU THR SEQRES 5 A 195 GLU GLU LEU ASP GLU ARG THR GLU LEU LEU LEU PHE GLU SEQRES 6 A 195 ALA SER ARG SER LYS LEU ILE GLU GLU LYS ILE ILE PRO SEQRES 7 A 195 ASP LEU LYS ARG ASP LYS VAL VAL ILE LEU ASP ARG PHE SEQRES 8 A 195 VAL LEU SER THR ILE ALA TYR GLN GLY TYR GLY LYS GLY SEQRES 9 A 195 LEU ASP VAL GLU PHE ILE LYS ASN LEU ASN GLU PHE ALA SEQRES 10 A 195 THR ARG GLY VAL LYS PRO ASP ILE THR LEU LEU LEU ASP SEQRES 11 A 195 ILE PRO VAL ASP ILE ALA LEU ARG ARG LEU LYS GLU LYS SEQRES 12 A 195 ASN ARG PHE GLU ASN LYS GLU PHE LEU GLU LYS VAL ARG SEQRES 13 A 195 LYS GLY PHE LEU GLU LEU ALA LYS GLU GLU GLU ASN VAL SEQRES 14 A 195 VAL VAL ILE ASP ALA SER GLY GLU GLU GLU GLU VAL PHE SEQRES 15 A 195 LYS GLU ILE LEU ARG ALA LEU SER GLY VAL LEU ARG VAL SEQRES 1 B 195 MET LEU ILE ALA PHE GLU GLY ILE ASP GLY SER GLY LYS SEQRES 2 B 195 THR THR GLN ALA LYS LYS LEU TYR GLU TYR LEU LYS GLN SEQRES 3 B 195 LYS GLY TYR PHE VAL SER LEU TYR ARG GLU PRO GLY GLY SEQRES 4 B 195 THR LYS VAL GLY GLU VAL LEU ARG GLU ILE LEU LEU THR SEQRES 5 B 195 GLU GLU LEU ASP GLU ARG THR GLU LEU LEU LEU PHE GLU SEQRES 6 B 195 ALA SER ARG SER LYS LEU ILE GLU GLU LYS ILE ILE PRO SEQRES 7 B 195 ASP LEU LYS ARG ASP LYS VAL VAL ILE LEU ASP ARG PHE SEQRES 8 B 195 VAL LEU SER THR ILE ALA TYR GLN GLY TYR GLY LYS GLY SEQRES 9 B 195 LEU ASP VAL GLU PHE ILE LYS ASN LEU ASN GLU PHE ALA SEQRES 10 B 195 THR ARG GLY VAL LYS PRO ASP ILE THR LEU LEU LEU ASP SEQRES 11 B 195 ILE PRO VAL ASP ILE ALA LEU ARG ARG LEU LYS GLU LYS SEQRES 12 B 195 ASN ARG PHE GLU ASN LYS GLU PHE LEU GLU LYS VAL ARG SEQRES 13 B 195 LYS GLY PHE LEU GLU LEU ALA LYS GLU GLU GLU ASN VAL SEQRES 14 B 195 VAL VAL ILE ASP ALA SER GLY GLU GLU GLU GLU VAL PHE SEQRES 15 B 195 LYS GLU ILE LEU ARG ALA LEU SER GLY VAL LEU ARG VAL HET MG A 201 1 HET ATP A 202 31 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET C5P A 206 21 HET MG B 201 1 HET ATP B 202 31 HET C5P B 203 21 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MG 2(MG 2+) FORMUL 4 ATP 2(C10 H16 N5 O13 P3) FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 C5P 2(C9 H14 N3 O8 P) FORMUL 12 HOH *63(H2 O) HELIX 1 AA1 GLY A 12 LYS A 27 1 16 HELIX 2 AA2 THR A 40 GLU A 53 1 14 HELIX 3 AA3 ASP A 56 LYS A 75 1 20 HELIX 4 AA4 LYS A 75 ARG A 82 1 8 HELIX 5 AA5 PHE A 91 GLY A 100 1 10 HELIX 6 AA6 ASP A 106 ARG A 119 1 14 HELIX 7 AA7 PRO A 132 LYS A 143 1 12 HELIX 8 AA8 ASN A 148 GLU A 166 1 19 HELIX 9 AA9 GLU A 177 GLY A 191 1 15 HELIX 10 AB1 GLY B 12 LYS B 27 1 16 HELIX 11 AB2 THR B 40 GLU B 53 1 14 HELIX 12 AB3 ASP B 56 LYS B 75 1 20 HELIX 13 AB4 LYS B 75 ARG B 82 1 8 HELIX 14 AB5 PHE B 91 GLY B 100 1 10 HELIX 15 AB6 ASP B 106 THR B 118 1 13 HELIX 16 AB7 PRO B 132 LYS B 143 1 12 HELIX 17 AB8 ASN B 148 GLU B 166 1 19 HELIX 18 AB9 GLU B 177 GLY B 191 1 15 SHEET 1 AA1 5 VAL A 31 ARG A 35 0 SHEET 2 AA1 5 VAL A 85 ASP A 89 1 O ILE A 87 N SER A 32 SHEET 3 AA1 5 LEU A 2 GLU A 6 1 N ILE A 3 O VAL A 86 SHEET 4 AA1 5 ILE A 125 ASP A 130 1 O LEU A 127 N ALA A 4 SHEET 5 AA1 5 VAL A 169 ASP A 173 1 O ILE A 172 N LEU A 128 SHEET 1 AA2 5 VAL B 31 ARG B 35 0 SHEET 2 AA2 5 VAL B 85 ASP B 89 1 O ASP B 89 N TYR B 34 SHEET 3 AA2 5 LEU B 2 GLU B 6 1 N ILE B 3 O VAL B 86 SHEET 4 AA2 5 ILE B 125 ASP B 130 1 O LEU B 127 N ALA B 4 SHEET 5 AA2 5 VAL B 169 ASP B 173 1 O ILE B 172 N LEU B 128 LINK OG1 THR A 14 MG MG A 201 1555 1555 2.10 LINK MG MG A 201 O1G ATP A 202 1555 1555 2.06 LINK MG MG A 201 O1B ATP A 202 1555 1555 2.55 LINK MG MG A 201 O HOH A 308 1555 1555 2.59 LINK MG MG A 201 O HOH A 314 1555 1555 2.21 LINK OG1 THR B 14 MG MG B 201 1555 1555 2.11 LINK MG MG B 201 O1G ATP B 202 1555 1555 2.07 LINK MG MG B 201 O1B ATP B 202 1555 1555 2.42 LINK MG MG B 201 O1P C5P B 203 1555 1555 2.83 CISPEP 1 GLU A 36 PRO A 37 0 -7.74 CISPEP 2 GLU B 36 PRO B 37 0 -7.15 SITE 1 AC1 5 THR A 14 ATP A 202 C5P A 206 HOH A 308 SITE 2 AC1 5 HOH A 314 SITE 1 AC2 18 ILE A 8 ASP A 9 GLY A 10 SER A 11 SITE 2 AC2 18 GLY A 12 LYS A 13 THR A 14 THR A 15 SITE 3 AC2 18 ARG A 90 ARG A 139 ARG A 145 GLY A 176 SITE 4 AC2 18 GLU A 177 GLU A 178 MG A 201 C5P A 206 SITE 5 AC2 18 HOH A 308 HOH A 309 SITE 1 AC3 2 VAL A 31 LYS A 84 SITE 1 AC4 3 ARG A 58 GLU B 115 ARG B 119 SITE 1 AC5 2 ARG A 119 ARG B 58 SITE 1 AC6 12 ASP A 9 ARG A 47 PHE A 64 ARG A 90 SITE 2 AC6 12 SER A 94 THR A 95 TYR A 98 GLN A 99 SITE 3 AC6 12 ARG A 145 MG A 201 ATP A 202 HOH A 301 SITE 1 AC7 3 THR B 14 ATP B 202 C5P B 203 SITE 1 AC8 17 ILE B 8 ASP B 9 GLY B 10 SER B 11 SITE 2 AC8 17 GLY B 12 LYS B 13 THR B 14 THR B 15 SITE 3 AC8 17 ARG B 90 ARG B 139 GLY B 176 GLU B 177 SITE 4 AC8 17 GLU B 178 MG B 201 C5P B 203 HOH B 314 SITE 5 AC8 17 HOH B 322 SITE 1 AC9 11 ASP B 9 ARG B 47 PHE B 64 ARG B 90 SITE 2 AC9 11 SER B 94 THR B 95 TYR B 98 GLN B 99 SITE 3 AC9 11 MG B 201 ATP B 202 HOH B 302 CRYST1 42.840 51.863 53.595 92.00 92.30 112.22 P 1 2 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 0.023343 0.009537 0.001457 0.00000 SCALE2 0.000000 0.020829 0.001128 0.00000 SCALE3 0.000000 0.000000 0.018701 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 -0.000759 -0.000004 22.60571 1 MTRIX2 2 0.000144 -0.195131 0.980777 30.31996 1 MTRIX3 2 -0.000745 0.980777 0.195131 -24.71533 1