HEADER TRANSFERASE 15-AUG-18 6AGY TITLE ASPERGILLUS FUMIGATUS AF293 NDK COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NDP KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS FUMIGATUS AF293; SOURCE 3 ORGANISM_COMMON: ASPERGILLUS FUMIGATUS; SOURCE 4 ORGANISM_TAXID: 330879; SOURCE 5 STRAIN: AF293; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU,L.HAN REVDAT 2 22-NOV-23 6AGY 1 REMARK REVDAT 1 13-MAR-19 6AGY 0 JRNL AUTH Y.HU,X.JIA,Z.LU,L.HAN JRNL TITL CHARACTERIZATION OF CRYSTAL STRUCTURE AND KEY RESIDUES OF JRNL TITL 2 ASPERGILLUS FUMIGATUS NUCLEOSIDE DIPHOSPHATE KINASE. JRNL REF BIOCHEM. BIOPHYS. RES. V. 511 148 2019 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 30773256 JRNL DOI 10.1016/J.BBRC.2019.01.126 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 13936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1400 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 26.5504 - 3.8739 0.98 1307 146 0.1562 0.1646 REMARK 3 2 3.8739 - 3.0763 1.00 1285 143 0.1293 0.1467 REMARK 3 3 3.0763 - 2.6879 0.99 1287 138 0.1423 0.1895 REMARK 3 4 2.6879 - 2.4423 0.99 1268 143 0.1349 0.1691 REMARK 3 5 2.4423 - 2.2674 0.98 1252 139 0.1249 0.1665 REMARK 3 6 2.2674 - 2.1337 0.98 1256 139 0.1278 0.1657 REMARK 3 7 2.1337 - 2.0269 0.98 1239 138 0.1284 0.1860 REMARK 3 8 2.0269 - 1.9387 0.98 1249 139 0.1215 0.1687 REMARK 3 9 1.9387 - 1.8641 0.95 1200 137 0.1396 0.2060 REMARK 3 10 1.8641 - 1.7998 0.94 1193 138 0.1546 0.1980 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 1190 REMARK 3 ANGLE : 0.799 1612 REMARK 3 CHIRALITY : 0.051 175 REMARK 3 PLANARITY : 0.005 207 REMARK 3 DIHEDRAL : 8.968 708 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 6AGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5420 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX SX-165MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14227 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.07438 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.5700 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43990 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.080 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: 4FKX REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 6.8, 1.2M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X+Y,Y,-Z REMARK 290 6555 X,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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 -0.500000 -0.866025 0.000000 35.37800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 61.27649 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -35.37800 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 61.27649 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 35.37800 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 61.27649 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -35.37800 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 61.27649 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 266 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 356 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 372 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 GLU A 151 REMARK 465 LYS A 152 REMARK 465 ALA A 153 REMARK 465 LEU A 154 REMARK 465 GLU A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 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 VAL A 115 -32.53 76.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 6AGY A 1 153 UNP Q7Z8P9 NDK_ASPFU 1 153 SEQADV 6AGY LEU A 154 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY GLU A 155 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 156 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 157 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 158 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 159 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 160 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6AGY HIS A 161 UNP Q7Z8P9 EXPRESSION TAG SEQRES 1 A 161 MET SER ASN GLU GLN THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 A 161 GLY VAL GLN ARG GLY LEU ILE GLY PRO ILE ILE SER ARG SEQRES 3 A 161 PHE GLU ASN ARG GLY PHE LYS LEU VAL ALA MET LYS LEU SEQRES 4 A 161 VAL SER PRO PRO GLN SER GLN LEU GLU GLN HIS TYR ALA SEQRES 5 A 161 ASP LEU SER ASP LYS PRO PHE PHE LYS GLY LEU VAL SER SEQRES 6 A 161 TYR MET LEU SER GLY PRO ILE CYS ALA MET VAL TRP GLU SEQRES 7 A 161 GLY ARG ASP VAL VAL LYS THR GLY ARG THR ILE LEU GLY SEQRES 8 A 161 ALA THR ASN PRO LEU ALA SER ALA PRO GLY THR ILE ARG SEQRES 9 A 161 GLY ASP PHE ALA ILE ASP VAL GLY ARG ASN VAL CYS HIS SEQRES 10 A 161 GLY SER ASP SER VAL GLU ASN ALA LYS LYS GLU ILE ALA SEQRES 11 A 161 LEU TRP PHE LYS PRO GLU GLU LEU ILE SER TRP LYS SER SEQRES 12 A 161 ALA THR PHE ASP TRP VAL TYR GLU LYS ALA LEU GLU HIS SEQRES 13 A 161 HIS HIS HIS HIS HIS FORMUL 2 HOH *184(H2 O) HELIX 1 AA1 LYS A 11 ARG A 17 1 7 HELIX 2 AA2 LEU A 19 GLY A 31 1 13 HELIX 3 AA3 PRO A 43 TYR A 51 1 9 HELIX 4 AA4 ALA A 52 SER A 55 5 4 HELIX 5 AA5 PHE A 59 LEU A 68 1 10 HELIX 6 AA6 ASP A 81 GLY A 91 1 11 HELIX 7 AA7 ASN A 94 SER A 98 5 5 HELIX 8 AA8 THR A 102 ALA A 108 1 7 HELIX 9 AA9 ASP A 110 ASN A 114 5 5 HELIX 10 AB1 SER A 121 PHE A 133 1 13 HELIX 11 AB2 LYS A 134 LEU A 138 5 5 HELIX 12 AB3 THR A 145 TYR A 150 1 6 SHEET 1 AA1 4 LYS A 33 VAL A 40 0 SHEET 2 AA1 4 ILE A 72 GLU A 78 -1 O ILE A 72 N VAL A 40 SHEET 3 AA1 4 GLN A 5 ILE A 10 -1 N ILE A 10 O CYS A 73 SHEET 4 AA1 4 CYS A 116 GLY A 118 -1 O HIS A 117 N ALA A 9 CRYST1 70.756 70.756 53.095 90.00 90.00 120.00 P 3 1 2 6 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 0.014133 0.008160 0.000000 0.00000 SCALE2 0.000000 0.016319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018834 0.00000