HEADER TRANSFERASE 22-APR-23 8J5E TITLE CRYSTAL STRUCTURE OF KINASE ABMG IN COMPLEX WITH 4'-THIOCYTIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYADENOSINE/DEOXYCYTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ABMG; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: AUTHOR'S PROVIDED SAMPLE SEQUENCE CORRESPONDS TO THE COMPND 7 REFERENCE SEQUENCE (A0A370RDE4) IN THE UNIPROT DATABASE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. ATCC 700974; SOURCE 3 ORGANISM_TAXID: 668825; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALBOMYCIN, BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.USHIMARU,T.MORI,H.-W.LIU,I.ABE REVDAT 1 24-APR-24 8J5E 0 JRNL AUTH R.USHIMARU,T.MORI,H.-W.LIU,I.ABE JRNL TITL CRYSTAL STRUCTURE OF KINASE ABMG IN COMPLEX WITH JRNL TITL 2 4'-THIOCYTIDINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.4700 - 4.1000 1.00 1824 152 0.1744 0.2038 REMARK 3 2 4.1000 - 3.2500 1.00 1742 146 0.1491 0.1813 REMARK 3 3 3.2500 - 2.8400 1.00 1725 144 0.1708 0.2203 REMARK 3 4 2.8400 - 2.5800 1.00 1729 144 0.1862 0.2263 REMARK 3 5 2.5800 - 2.4000 1.00 1689 141 0.1736 0.2382 REMARK 3 6 2.4000 - 2.2500 1.00 1711 143 0.1717 0.2098 REMARK 3 7 2.2500 - 2.1400 1.00 1705 143 0.1526 0.2011 REMARK 3 8 2.1400 - 2.0500 1.00 1690 141 0.1615 0.2035 REMARK 3 9 2.0500 - 1.9700 1.00 1691 141 0.1732 0.2316 REMARK 3 10 1.9700 - 1.9000 1.00 1694 142 0.1817 0.2271 REMARK 3 11 1.9000 - 1.8400 1.00 1699 141 0.1833 0.2331 REMARK 3 12 1.8400 - 1.7900 1.00 1681 142 0.1865 0.2453 REMARK 3 13 1.7900 - 1.7400 1.00 1683 140 0.1965 0.2533 REMARK 3 14 1.7400 - 1.7000 0.99 1676 140 0.2062 0.2581 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.168 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.735 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1899 REMARK 3 ANGLE : 0.981 2575 REMARK 3 CHIRALITY : 0.056 286 REMARK 3 PLANARITY : 0.008 340 REMARK 3 DIHEDRAL : 4.960 269 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8J5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300037194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.68200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM NITRATE, 28% PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.04450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.04450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.32100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.05400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.32100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.05400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.04450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.32100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.05400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.04450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.32100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.05400 REMARK 290 SMTRY3 8 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 ASP A 10 REMARK 465 ARG A 11 REMARK 465 LEU A 12 REMARK 465 LYS A 13 REMARK 465 ALA A 14 REMARK 465 VAL A 15 REMARK 465 GLY A 28 REMARK 465 GLY A 29 REMARK 465 ARG A 30 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 16 CG CD OE1 OE2 REMARK 470 ASP A 26 CG OD1 OD2 REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 GLU A 174 CG CD OE1 OE2 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 A 26 58.75 -119.04 REMARK 500 ASP A 219 34.64 -141.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 660 DISTANCE = 8.11 ANGSTROMS DBREF1 8J5E A 8 253 UNP A0A370RDE4_9ACTN DBREF2 8J5E A A0A370RDE4 8 253 SEQADV 8J5E SER A 7 UNP A0A370RDE EXPRESSION TAG SEQRES 1 A 247 SER THR SER ASP ARG LEU LYS ALA VAL GLU GLN ASN LEU SEQRES 2 A 247 TYR ASP VAL GLY PRO ARG ASP SER GLY GLY ARG GLU GLY SEQRES 3 A 247 PRO GLY HIS TYR ILE ALA ILE SER GLY ASN THR ALA ALA SEQRES 4 A 247 GLY LYS THR THR LEU ILE GLU THR LEU ALA GLY SER LEU SEQRES 5 A 247 ARG ALA ALA GLY ALA ASP ALA VAL GLY VAL SER GLU ARG SEQRES 6 A 247 VAL PHE HIS HIS ARG TYR LEU LYS LEU MET PHE SER ALA SEQRES 7 A 247 SER ALA ASP PHE ALA PHE PRO ILE GLN LEU SER PHE MET SEQRES 8 A 247 LEU GLU ARG HIS LEU LEU LEU LEU ASP ASN LEU VAL ARG SEQRES 9 A 247 ARG GLY ARG THR MET VAL MET GLU ARG SER HIS LEU ASP SEQRES 10 A 247 ASP ALA MET PHE VAL ARG GLU HIS VAL ALA SER GLY ALA SEQRES 11 A 247 ILE THR ALA ALA GLN GLN ARG ALA TYR THR GLU VAL SER SEQRES 12 A 247 GLY GLU LEU ASN ALA ARG ILE PRO ASN PRO ASP LEU ILE SEQRES 13 A 247 VAL LEU MET ASN PRO GLU PRO GLU LEU SER LEU GLU ARG SEQRES 14 A 247 LEU ALA ARG ALA GLU ALA GLU GLY SER ARG PRO ARG GLU SEQRES 15 A 247 PHE PRO SER ASP ALA ALA LYS ARG ALA TRP VAL HIS ARG SEQRES 16 A 247 TRP TYR ASP LEU TYR GLN GLU LEU HIS ASP ASP TYR ARG SEQRES 17 A 247 ARG ARG ALA VAL ASP GLY ASP LEU ARG GLY THR GLU LEU SEQRES 18 A 247 LEU GLU LEU ASP ALA ALA ALA SER PRO GLU GLU LYS ILE SEQRES 19 A 247 ALA THR VAL THR ALA ARG ALA ARG SER LEU VAL VAL GLY HET TQR A 301 17 HETNAM TQR 4-AZANYL-1-[(2~{R},3~{R},4~{S},5~{R})-5- HETNAM 2 TQR (HYDROXYMETHYL)-3,4-BIS(OXIDANYL)THIOLAN-2- HETNAM 3 TQR YL]PYRIMIDIN-2-ONE FORMUL 2 TQR C9 H13 N3 O4 S FORMUL 3 HOH *260(H2 O) HELIX 1 AA1 LYS A 47 ALA A 61 1 15 HELIX 2 AA2 SER A 69 PHE A 73 5 5 HELIX 3 AA3 LEU A 78 ALA A 84 1 7 HELIX 4 AA4 ALA A 84 LEU A 108 1 25 HELIX 5 AA5 ASP A 123 SER A 134 1 12 HELIX 6 AA6 THR A 138 ALA A 154 1 17 HELIX 7 AA7 GLU A 168 GLU A 182 1 15 HELIX 8 AA8 SER A 191 GLY A 220 1 30 HELIX 9 AA9 SER A 235 SER A 249 1 15 SHEET 1 AA1 5 ALA A 65 VAL A 68 0 SHEET 2 AA1 5 THR A 114 MET A 117 1 O VAL A 116 N VAL A 66 SHEET 3 AA1 5 TYR A 36 SER A 40 1 N ILE A 37 O MET A 117 SHEET 4 AA1 5 LEU A 161 LEU A 164 1 O VAL A 163 N ALA A 38 SHEET 5 AA1 5 GLU A 226 GLU A 229 1 O LEU A 228 N ILE A 162 CRYST1 70.642 78.108 84.089 90.00 90.00 90.00 C 2 2 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 0.014156 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011892 0.00000