PDB Short entry for 1XSC HEADER HYDROLASE 18-OCT-04 1XSC TITLE STRUCTURE OF THE NUDIX ENZYME AP4A HYDROLASE FROM HOMO SAPIENS (E63A TITLE 2 MUTANT) IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE ASYMMETRICAL COMPND 5 HYDROLASE, DIADENOSINE TETRAPHOSPHATASE, AP4A HYDROLASE, AP4AASE; COMPND 6 EC: 3.6.1.17; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6-P3 KEYWDS NUDIX ENZYME, HUMAN AP4A ATP HYDROLASE, ALPHA-BETA, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR J.D.SWARBRICK,S.BUYYA,D.GUNAWARDANA,K.R.GAYLER,A.G.MCLENNAN, AUTHOR 2 P.R.GOOLEY REVDAT 4 10-NOV-21 1XSC 1 REMARK SEQADV REVDAT 3 24-FEB-09 1XSC 1 VERSN REVDAT 2 22-MAR-05 1XSC 1 JRNL AUTHOR REVDAT 1 21-DEC-04 1XSC 0 JRNL AUTH J.D.SWARBRICK,S.BUYYA,D.GUNAWARDANA,K.R.GAYLER,A.G.MCLENNAN, JRNL AUTH 2 P.R.GOOLEY JRNL TITL STRUCTURE AND SUBSTRATE-BINDING MECHANISM OF HUMAN AP4A JRNL TITL 2 HYDROLASE JRNL REF J.BIOL.CHEM. V. 280 8471 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15596429 JRNL DOI 10.1074/JBC.M412318200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XSC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030711. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 51MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0MM HUMAN AP4A HYDROLASE, 13C REMARK 210 15N ATP; 1.0MM HUMAN AP4A REMARK 210 HYDROLASE, 13C 15N ATP REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 13C REMARK 210 NOESY OVER AROMATIC/ANOMERIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : CNS FROM A STARTING STRUCTURE REMARK 210 WITH ATP 20A FROM BINDING SITE, REMARK 210 REFINE AGAINST NOE/CACB NO RAMA REMARK 210 POTENTIAL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS CALCUALTION INCLUDES ATP CONSTRAINTS. REMARK 210 SLOW COOLING, LOWER TEMPERATURE (20000K RATHER THAN 50000K) ATP REMARK 210 STARTS 20A FROM LOWEST ENERGY CONFORMER REMARK 210 RESIDUES 1 AND 2 ARE CHANGED FROM GP TO ALANINE IN THE REMARK 210 CALCULATIONS. THESE ARE FROM THE NON NATIVE PRECISSION CLEAVAGE REMARK 210 SITE AND ARE UNSTRUCTRUED. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-25 REMARK 470 RES CSSEQI ATOMS REMARK 470 LEU A 153 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H PHE A 16 O ALA A 101 1.54 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 1 ALA A 7 167.41 71.10 REMARK 500 1 LEU A 20 -82.85 -55.24 REMARK 500 1 LYS A 23 -78.33 -106.43 REMARK 500 1 ASN A 26 -75.06 -111.57 REMARK 500 1 ALA A 28 -37.07 177.19 REMARK 500 1 ASP A 38 -175.30 -171.00 REMARK 500 1 PRO A 46 99.53 -60.30 REMARK 500 1 ALA A 68 -14.55 -153.25 REMARK 500 1 ALA A 89 -93.75 -70.78 REMARK 500 1 ASN A 91 30.23 -171.47 REMARK 500 1 GLN A 132 -34.11 -37.80 REMARK 500 1 ILE A 150 -142.30 -95.74 REMARK 500 1 GLU A 151 -68.52 -142.90 REMARK 500 1 ALA A 152 -42.59 -163.76 REMARK 500 2 MET A 6 172.90 -58.27 REMARK 500 2 ALA A 7 163.60 66.99 REMARK 500 2 LEU A 20 -82.36 -59.83 REMARK 500 2 LYS A 23 -78.49 -110.84 REMARK 500 2 ASN A 26 -71.60 -110.74 REMARK 500 2 PRO A 45 169.08 -49.17 REMARK 500 2 ALA A 68 -7.96 -148.24 REMARK 500 2 ALA A 89 -98.73 -77.29 REMARK 500 2 ASN A 91 27.80 176.79 REMARK 500 2 SER A 113 -156.27 -89.09 REMARK 500 2 GLN A 132 -34.06 -37.57 REMARK 500 2 ILE A 150 -124.76 -67.24 REMARK 500 2 GLU A 151 -60.40 -97.10 REMARK 500 3 PRO A 2 26.32 -72.32 REMARK 500 3 LEU A 3 -176.01 59.56 REMARK 500 3 ALA A 7 167.51 59.26 REMARK 500 3 LEU A 20 -81.01 -59.07 REMARK 500 3 LYS A 23 -78.70 -110.53 REMARK 500 3 ASN A 27 -75.57 -110.57 REMARK 500 3 ALA A 28 -65.91 65.41 REMARK 500 3 PRO A 46 96.24 -61.49 REMARK 500 3 ALA A 68 -8.99 -144.59 REMARK 500 3 ALA A 89 -95.59 -76.62 REMARK 500 3 ASN A 91 29.11 176.41 REMARK 500 3 ALA A 118 -179.57 -171.24 REMARK 500 3 GLN A 132 -32.26 -38.76 REMARK 500 3 ILE A 150 -136.62 -94.67 REMARK 500 3 GLU A 151 -62.62 -100.90 REMARK 500 4 MET A 6 159.38 59.19 REMARK 500 4 ALA A 7 164.69 58.74 REMARK 500 4 LYS A 23 -80.08 -138.91 REMARK 500 4 ASN A 26 -71.11 -91.47 REMARK 500 4 ASP A 38 -165.16 -173.22 REMARK 500 4 PRO A 46 83.51 -60.34 REMARK 500 4 ALA A 89 -106.34 -75.43 REMARK 500 4 ASN A 91 30.10 178.25 REMARK 500 REMARK 500 THIS ENTRY HAS 368 RAMACHANDRAN OUTLIERS. 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 ATP A 154 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XSA RELATED DB: PDB REMARK 900 THE SAME PROTEIN(E63A) OF APO STRUCTURE REMARK 900 RELATED ID: 1XSB RELATED DB: PDB REMARK 900 THE SAME PROTEIN(E63A) OF ATP STRUCTURE IN COMPLEX WITH ATP DBREF 1XSC A 7 152 UNP P50583 AP4A_HUMAN 1 146 SEQADV 1XSC GLY A 1 UNP P50583 CLONING ARTIFACT SEQADV 1XSC PRO A 2 UNP P50583 CLONING ARTIFACT SEQADV 1XSC LEU A 3 UNP P50583 CLONING ARTIFACT SEQADV 1XSC GLY A 4 UNP P50583 CLONING ARTIFACT SEQADV 1XSC SER A 5 UNP P50583 CLONING ARTIFACT SEQADV 1XSC MET A 6 UNP P50583 CLONING ARTIFACT SEQADV 1XSC ALA A 63 UNP P50583 GLU 57 ENGINEERED MUTATION SEQADV 1XSC LEU A 153 UNP P50583 CLONING ARTIFACT SEQRES 1 A 153 GLY PRO LEU GLY SER MET ALA LEU ARG ALA CYS GLY LEU SEQRES 2 A 153 ILE ILE PHE ARG ARG CYS LEU ILE PRO LYS VAL ASP ASN SEQRES 3 A 153 ASN ALA ILE GLU PHE LEU LEU LEU GLN ALA SER ASP GLY SEQRES 4 A 153 ILE HIS HIS TRP THR PRO PRO LYS GLY HIS VAL GLU PRO SEQRES 5 A 153 GLY GLU ASP ASP LEU GLU THR ALA LEU ARG ALA THR GLN SEQRES 6 A 153 GLU GLU ALA GLY ILE GLU ALA GLY GLN LEU THR ILE ILE SEQRES 7 A 153 GLU GLY PHE LYS ARG GLU LEU ASN TYR VAL ALA ARG ASN SEQRES 8 A 153 LYS PRO LYS THR VAL ILE TYR TRP LEU ALA GLU VAL LYS SEQRES 9 A 153 ASP TYR ASP VAL GLU ILE ARG LEU SER HIS GLU HIS GLN SEQRES 10 A 153 ALA TYR ARG TRP LEU GLY LEU GLU GLU ALA CYS GLN LEU SEQRES 11 A 153 ALA GLN PHE LYS GLU MET LYS ALA ALA LEU GLN GLU GLY SEQRES 12 A 153 HIS GLN PHE LEU CYS SER ILE GLU ALA LEU HET ATP A 154 42 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 HELIX 1 1 ASP A 55 ALA A 68 1 14 HELIX 2 2 GLU A 71 LEU A 75 5 5 HELIX 3 3 GLY A 123 ALA A 131 1 9 HELIX 4 4 PHE A 133 CYS A 148 1 16 SHEET 1 A 4 LYS A 47 GLY A 48 0 SHEET 2 A 4 LEU A 8 ILE A 15 -1 O CYS A 11 N GLY A 48 SHEET 3 A 4 PRO A 93 ALA A 101 1 O PRO A 93 N LEU A 8 SHEET 4 A 4 ARG A 83 VAL A 88 -1 O ARG A 83 N TYR A 98 SHEET 1 B 3 TRP A 43 THR A 44 0 SHEET 2 B 3 PHE A 31 ALA A 36 -1 O LEU A 34 N THR A 44 SHEET 3 B 3 HIS A 116 LEU A 122 -1 N GLN A 117 O GLN A 35 SITE 1 AC1 5 HIS A 42 TYR A 87 ALA A 89 PHE A 133 SITE 2 AC1 5 GLU A 135 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000