HEADER TRANSFERASE 22-APR-23 8J5F TITLE CRYSTAL STRUCTURE OF KINASE ABMG IN COMPLEX WITH CYTIDINE AND ADP 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 8J5F 0 JRNL AUTH R.USHIMARU,T.MORI,H.-W.LIU,I.ABE JRNL TITL CRYSTAL STRUCTURE OF KINASE ABMG IN COMPLEX WITH CYTIDINE JRNL TITL 2 AND ADP 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) : 44.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.550 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 44.8400 - 4.1000 1.00 1857 151 0.1482 0.1876 REMARK 3 2 4.1000 - 3.2500 1.00 1797 147 0.1314 0.1505 REMARK 3 3 3.2500 - 2.8400 1.00 1755 144 0.1495 0.1883 REMARK 3 4 2.8400 - 2.5800 1.00 1765 144 0.1549 0.1961 REMARK 3 5 2.5800 - 2.4000 1.00 1732 141 0.1450 0.2007 REMARK 3 6 2.4000 - 2.2600 1.00 1727 142 0.1458 0.1911 REMARK 3 7 2.2500 - 2.1400 1.00 1745 142 0.1383 0.2174 REMARK 3 8 2.1400 - 2.0500 1.00 1740 142 0.1381 0.1766 REMARK 3 9 2.0500 - 1.9700 1.00 1733 142 0.1463 0.2128 REMARK 3 10 1.9700 - 1.9000 1.00 1716 140 0.1674 0.2314 REMARK 3 11 1.9000 - 1.8400 1.00 1718 140 0.1800 0.2064 REMARK 3 12 1.8400 - 1.7900 1.00 1747 143 0.1728 0.2298 REMARK 3 13 1.7900 - 1.7400 1.00 1722 140 0.1941 0.2300 REMARK 3 14 1.7400 - 1.7000 1.00 1726 142 0.2607 0.3257 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) : 0.172 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.035 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.02 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 1945 REMARK 3 ANGLE : 0.973 2645 REMARK 3 CHIRALITY : 0.050 291 REMARK 3 PLANARITY : 0.009 347 REMARK 3 DIHEDRAL : 5.084 275 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 8J5F 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_1300037249. 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) : 1.0 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 : 26511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.96800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 43.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M CITRATE, 0.07 M BIS-TRIS REMARK 280 PROPANE, 28% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 41.66600 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 41.66600 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 35.98500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.49300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.98500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.49300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.66600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.98500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.49300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.66600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.98500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.49300 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: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 208 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 ARG A 119 164.71 71.01 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8J5F A 8 253 UNP A0A370RDE4_9ACTN DBREF2 8J5F A A0A370RDE4 8 253 SEQADV 8J5F 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 CTN A 301 17 HET ADP A 302 27 HETNAM CTN 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN CTN CYTIDINE FORMUL 2 CTN C9 H13 N3 O5 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 HOH *327(H2 O) HELIX 1 AA1 GLY A 46 ALA A 61 1 16 HELIX 2 AA2 SER A 69 PHE A 73 5 5 HELIX 3 AA3 TYR A 77 ALA A 84 1 8 HELIX 4 AA4 ALA A 84 LEU A 108 1 25 HELIX 5 AA5 ASP A 123 GLY A 135 1 13 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 ARG A 248 1 14 HELIX 10 AB1 SER A 249 VAL A 251 5 3 SHEET 1 AA1 5 ALA A 65 VAL A 68 0 SHEET 2 AA1 5 THR A 114 GLU A 118 1 O VAL A 116 N VAL A 68 SHEET 3 AA1 5 TYR A 36 SER A 40 1 N ILE A 37 O MET A 115 SHEET 4 AA1 5 LEU A 161 LEU A 164 1 O VAL A 163 N SER A 40 SHEET 5 AA1 5 GLU A 226 GLU A 229 1 O LEU A 228 N LEU A 164 CRYST1 71.970 78.986 83.332 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 0.013895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012000 0.00000