HEADER HYDROLASE 18-MAY-12 4F95 TITLE CRYSTAL STRUCTURE OF HUMAN INOSINE TRIPHOSPHATE PYROPHOSPHATASE P32T TITLE 2 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSINE TRIPHOSPHATE PYROPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ITPASE, INOSINE TRIPHOSPHATASE, NON-CANONICAL PURINE NTP COMPND 5 PYROPHOSPHATASE, NON-STANDARD PURINE NTP PYROPHOSPHATASE, NUCLEOSIDE- COMPND 6 TRIPHOSPHATE DIPHOSPHATASE, NUCLEOSIDE-TRIPHOSPHATE PYROPHOSPHATASE, COMPND 7 NTPASE, PUTATIVE ONCOGENE PROTEIN HLC14-06-P; COMPND 8 EC: 3.6.1.19; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C20ORF37, ITPA, ITPA (P32T MUTANT), MY049, OK/SW-CL.9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.SIMONE,Y.I.PAVLOV,G.E.O.BORGSTAHL REVDAT 3 13-SEP-23 4F95 1 SEQADV REVDAT 2 12-JUN-13 4F95 1 JRNL REVDAT 1 10-APR-13 4F95 0 JRNL AUTH P.D.SIMONE,L.R.STRUBLE,A.KELLEZI,C.A.BROWN,C.E.GRABOW, JRNL AUTH 2 I.KHUTSISHVILI,L.A.MARKY,Y.I.PAVLOV,G.E.BORGSTAHL JRNL TITL THE HUMAN ITPA POLYMORPHIC VARIANT P32T IS DESTABILIZED BY JRNL TITL 2 THE UNPACKING OF THE HYDROPHOBIC CORE. JRNL REF J.STRUCT.BIOL. V. 182 197 2013 JRNL REFN ISSN 1047-8477 JRNL PMID 23528839 JRNL DOI 10.1016/J.JSB.2013.03.007 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10495 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 501 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 29.7387 - 3.2849 1.00 2631 124 0.2059 0.2551 REMARK 3 2 3.2849 - 2.6078 1.00 2486 129 0.2450 0.3628 REMARK 3 3 2.6078 - 2.2783 1.00 2460 121 0.2862 0.4070 REMARK 3 4 2.2783 - 2.0701 1.00 2417 127 0.3632 0.4034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 42.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.11610 REMARK 3 B22 (A**2) : -4.58890 REMARK 3 B33 (A**2) : 2.47280 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1547 REMARK 3 ANGLE : 1.252 2100 REMARK 3 CHIRALITY : 0.079 225 REMARK 3 PLANARITY : 0.005 280 REMARK 3 DIHEDRAL : 17.112 582 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 4F95 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072611. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.667 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC VARIMAX CONFOCAL MAX-FLUX REMARK 200 OPTIC REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10531 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 29.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.660 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.71 REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2I5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24.4% PEG 3350, 0.1 M BIS-TRIS, 10 MM REMARK 280 BETA-MERCAPTOETHANOL, PH 6.667, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 15.51000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.51000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.21000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 233 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 259 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 192 REMARK 465 ALA A 193 REMARK 465 ALA A 194 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OE2 GLU A 161 O HOH A 227 2.18 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 THR A 32 -12.10 76.75 REMARK 500 LYS A 96 163.08 69.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 30 PHE A 31 -36.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I5D RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN AT 1.63 ANGSTROMS. REMARK 900 RELATED ID: 2CAR RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN AT 1.09 ANGSTROMS. REMARK 900 RELATED ID: 2J4E RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN IN COMPLEX WITH ITP AT 2.80 ANGSTROMS DBREF 4F95 A 1 194 UNP Q9BY32 ITPA_HUMAN 1 194 SEQADV 4F95 GLY A -2 UNP Q9BY32 EXPRESSION TAG SEQADV 4F95 SER A -1 UNP Q9BY32 EXPRESSION TAG SEQADV 4F95 HIS A 0 UNP Q9BY32 EXPRESSION TAG SEQADV 4F95 THR A 32 UNP Q9BY32 PRO 32 ENGINEERED MUTATION SEQRES 1 A 197 GLY SER HIS MET ALA ALA SER LEU VAL GLY LYS LYS ILE SEQRES 2 A 197 VAL PHE VAL THR GLY ASN ALA LYS LYS LEU GLU GLU VAL SEQRES 3 A 197 VAL GLN ILE LEU GLY ASP LYS PHE THR CYS THR LEU VAL SEQRES 4 A 197 ALA GLN LYS ILE ASP LEU PRO GLU TYR GLN GLY GLU PRO SEQRES 5 A 197 ASP GLU ILE SER ILE GLN LYS CYS GLN GLU ALA VAL ARG SEQRES 6 A 197 GLN VAL GLN GLY PRO VAL LEU VAL GLU ASP THR CYS LEU SEQRES 7 A 197 CYS PHE ASN ALA LEU GLY GLY LEU PRO GLY PRO TYR ILE SEQRES 8 A 197 LYS TRP PHE LEU GLU LYS LEU LYS PRO GLU GLY LEU HIS SEQRES 9 A 197 GLN LEU LEU ALA GLY PHE GLU ASP LYS SER ALA TYR ALA SEQRES 10 A 197 LEU CYS THR PHE ALA LEU SER THR GLY ASP PRO SER GLN SEQRES 11 A 197 PRO VAL ARG LEU PHE ARG GLY ARG THR SER GLY ARG ILE SEQRES 12 A 197 VAL ALA PRO ARG GLY CYS GLN ASP PHE GLY TRP ASP PRO SEQRES 13 A 197 CYS PHE GLN PRO ASP GLY TYR GLU GLN THR TYR ALA GLU SEQRES 14 A 197 MET PRO LYS ALA GLU LYS ASN ALA VAL SER HIS ARG PHE SEQRES 15 A 197 ARG ALA LEU LEU GLU LEU GLN GLU TYR PHE GLY SER LEU SEQRES 16 A 197 ALA ALA FORMUL 2 HOH *68(H2 O) HELIX 1 1 ASN A 16 GLY A 28 1 13 HELIX 2 2 GLU A 48 GLN A 65 1 18 HELIX 3 3 ALA A 79 GLY A 81 5 3 HELIX 4 4 TYR A 87 LEU A 103 1 17 HELIX 5 5 TRP A 151 PRO A 153 5 3 HELIX 6 6 PRO A 168 SER A 176 1 9 HELIX 7 7 SER A 176 PHE A 189 1 14 SHEET 1 A 4 THR A 34 GLN A 38 0 SHEET 2 A 4 LYS A 9 VAL A 13 1 N ILE A 10 O THR A 34 SHEET 3 A 4 VAL A 68 PHE A 77 1 O LEU A 69 N VAL A 11 SHEET 4 A 4 PRO A 84 GLY A 85 -1 O GLY A 85 N LEU A 75 SHEET 1 B 6 THR A 34 GLN A 38 0 SHEET 2 B 6 LYS A 9 VAL A 13 1 N ILE A 10 O THR A 34 SHEET 3 B 6 VAL A 68 PHE A 77 1 O LEU A 69 N VAL A 11 SHEET 4 B 6 SER A 111 SER A 121 -1 O TYR A 113 N CYS A 76 SHEET 5 B 6 ARG A 130 ILE A 140 -1 O PHE A 132 N PHE A 118 SHEET 6 B 6 PHE A 155 PRO A 157 -1 O GLN A 156 N ARG A 139 CISPEP 1 ALA A 3 SER A 4 0 -4.71 CISPEP 2 ALA A 3 SER A 4 0 -5.98 CISPEP 3 LEU A 83 PRO A 84 0 -0.41 CRYST1 31.020 104.420 50.360 90.00 90.00 90.00 P 21 21 2 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 0.032237 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019857 0.00000