HEADER HYDROLASE 08-JUL-15 5CFJ TITLE STRUCTURAL AND FUNCTIONAL ATTRIBUTES OF MALARIA PARASITE AP4A TITLE 2 HYDROLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE (DIADENOSINE COMPND 3 TETRAPHOSPHATASE), PUTATIVE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: AP4A HYDROLASE; COMPND 6 EC: 3.6.1.17; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 3D7; SOURCE 5 GENE: PFE1035C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS AP4A, PURINERGIC SIGNALLING, PLASMODIUM, NUDIX HYDROLYSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SHARMA,M.YOGAVEL,A.SHARMA REVDAT 4 20-MAR-24 5CFJ 1 REMARK REVDAT 3 16-AUG-17 5CFJ 1 REMARK REVDAT 2 17-FEB-16 5CFJ 1 JRNL REVDAT 1 10-FEB-16 5CFJ 0 JRNL AUTH A.SHARMA,M.YOGAVEL,A.SHARMA JRNL TITL STRUCTURAL AND FUNCTIONAL ATTRIBUTES OF MALARIA PARASITE JRNL TITL 2 DIADENOSINE TETRAPHOSPHATE HYDROLASE JRNL REF SCI REP V. 6 19981 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26829485 JRNL DOI 10.1038/SREP19981 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 37464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1865 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 25.7184 - 2.9379 0.62 3236 170 0.1928 0.2195 REMARK 3 2 2.9379 - 2.3324 0.61 3169 159 0.1960 0.1939 REMARK 3 3 2.3324 - 2.0377 0.55 2853 150 0.1513 0.1629 REMARK 3 4 2.0377 - 1.8514 0.53 2717 143 0.1445 0.1749 REMARK 3 5 1.8514 - 1.7188 0.53 2756 145 0.1449 0.1798 REMARK 3 6 1.7188 - 1.6175 0.53 2746 144 0.1392 0.1593 REMARK 3 7 1.6175 - 1.5365 0.52 2699 142 0.1347 0.1820 REMARK 3 8 1.5365 - 1.4696 0.52 2703 142 0.1313 0.1527 REMARK 3 9 1.4696 - 1.4130 0.52 2722 144 0.1385 0.2109 REMARK 3 10 1.4130 - 1.3643 0.52 2660 140 0.1441 0.1955 REMARK 3 11 1.3643 - 1.3216 0.50 2608 137 0.1513 0.1833 REMARK 3 12 1.3216 - 1.2838 0.48 2522 133 0.1646 0.2113 REMARK 3 13 1.2838 - 1.2500 0.43 2208 116 0.1660 0.2238 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.34 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 : 0.006 1216 REMARK 3 ANGLE : 1.144 1654 REMARK 3 CHIRALITY : 0.040 176 REMARK 3 PLANARITY : 0.005 212 REMARK 3 DIHEDRAL : 13.248 458 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 5CFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULPHATE, SODIUM ACETATE, REMARK 280 ETHYLENE GLYCOL, PEG400, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 15.74550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.33850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.17400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.33850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.74550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.17400 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 LYS A 2 REMARK 465 ILE A 3 REMARK 465 VAL A 22 REMARK 465 THR A 23 REMARK 465 THR A 24 REMARK 465 GLY A 25 REMARK 465 ASP A 26 REMARK 465 ILE A 27 REMARK 465 GLU A 150 REMARK 465 GLN A 151 REMARK 465 LEU A 152 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 ASN A 4 CG OD1 ND2 REMARK 470 LYS A 7 CE NZ REMARK 470 LYS A 17 CD CE NZ REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 TYR A 19 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 19 OH REMARK 470 LYS A 29 CD CE NZ REMARK 470 TYR A 39 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ALA A 40 CB REMARK 470 LYS A 42 CB CG CD CE NZ REMARK 470 VAL A 89 CB CG1 CG2 REMARK 470 LYS A 90 CB CG CD CE NZ REMARK 470 ASP A 91 OD1 OD2 REMARK 470 LYS A 92 CG CD CE NZ 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 91 17.28 59.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XSC RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN AP4A HYDROLASE IN COMPLEX WITH ATP REMARK 900 RELATED ID: 5CFI RELATED DB: PDB DBREF 5CFJ A 1 152 UNP C0H4F3 C0H4F3_PLAF7 1 152 SEQRES 1 A 152 MET LYS ILE ASN ILE ILE LYS ALA PHE GLY ILE LEU LEU SEQRES 2 A 152 CYS ARG LEU LYS LYS TYR ASN PRO VAL THR THR GLY ASP SEQRES 3 A 152 ILE ASN LYS PHE GLU PHE LEU PHE LEU LYS ALA SER TYR SEQRES 4 A 152 ALA ASP LYS HIS TRP THR PRO PRO LYS GLY LEU HIS GLU SEQRES 5 A 152 ASN ASN GLU SER GLY LEU GLU THR ALA VAL ARG GLU THR SEQRES 6 A 152 LEU GLU GLU THR GLY ILE ASN LYS ASP LYS TYR LYS LEU SEQRES 7 A 152 LEU ASN TYR GLN LYS THR LEU LYS TYR ASN VAL LYS ASP SEQRES 8 A 152 LYS PRO LYS GLU THR THR TYR TYR LEU ALA MET LEU LEU SEQRES 9 A 152 ASN ASN GLU GLU ASN VAL ILE LEU SER ASP GLU HIS THR SEQRES 10 A 152 ASP TYR LYS TRP ILE GLY SER HIS GLU SER ASP THR TYR SEQRES 11 A 152 ASN LEU PRO GLU SER LEU ALA ASP LEU LEU LYS GLU ALA SEQRES 12 A 152 GLU GLU PHE LEU ASN LYS GLU GLN LEU HET SO4 A 201 5 HET SO4 A 202 10 HET SO4 A 203 5 HET PEG A 204 7 HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *122(H2 O) HELIX 1 AA1 SER A 56 GLY A 70 1 15 HELIX 2 AA2 ASN A 72 ASP A 74 5 3 HELIX 3 AA3 GLY A 123 SER A 127 5 5 HELIX 4 AA4 PRO A 133 ASN A 148 1 16 SHEET 1 AA1 5 TRP A 44 THR A 45 0 SHEET 2 AA1 5 PHE A 30 ALA A 37 -1 N LEU A 35 O THR A 45 SHEET 3 AA1 5 ILE A 6 LEU A 16 -1 N ARG A 15 O GLU A 31 SHEET 4 AA1 5 LYS A 92 LEU A 103 1 O LEU A 103 N CYS A 14 SHEET 5 AA1 5 TYR A 76 VAL A 89 -1 N LEU A 85 O THR A 96 SHEET 1 AA2 4 LYS A 48 LEU A 50 0 SHEET 2 AA2 4 ILE A 6 LEU A 16 -1 N PHE A 9 O GLY A 49 SHEET 3 AA2 4 PHE A 30 ALA A 37 -1 O GLU A 31 N ARG A 15 SHEET 4 AA2 4 HIS A 116 ILE A 122 -1 O LYS A 120 N PHE A 34 SITE 1 AC1 5 HIS A 43 LYS A 48 TYR A 87 LYS A 94 SITE 2 AC1 5 HOH A 307 SITE 1 AC2 7 ASN A 28 LYS A 36 LYS A 42 TRP A 44 SITE 2 AC2 7 HIS A 125 LYS A 141 HOH A 309 SITE 1 AC3 5 ARG A 15 TYR A 119 TRP A 121 HOH A 321 SITE 2 AC3 5 HOH A 389 SITE 1 AC4 4 LEU A 66 GLY A 70 LYS A 77 HOH A 338 CRYST1 31.491 44.348 94.677 90.00 90.00 90.00 P 21 21 21 4 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 0.031755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010562 0.00000