HEADER HYDROLASE 08-APR-11 3RGQ TITLE CRYSTAL STRUCTURE OF PTPMT1 IN COMPLEX WITH PI(5)P COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-TYROSINE PHOSPHATASE MITOCHONDRIAL 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTEN-LIKE PHOSPHATASE, PHOSPHOINOSITIDE LIPID PHOSPHATASE; COMPND 5 EC: 3.1.3.16, 3.1.3.48; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PLIP, PTPMT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS PHOSPHATIDYLGLYCEROL PHOSPHATE (PGP) PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.XIAO,J.L.ENGEL REVDAT 5 21-FEB-24 3RGQ 1 REMARK SEQADV REVDAT 4 08-NOV-17 3RGQ 1 REMARK REVDAT 3 03-AUG-11 3RGQ 1 JRNL REVDAT 2 20-JUL-11 3RGQ 1 JRNL REVDAT 1 06-JUL-11 3RGQ 0 JRNL AUTH J.XIAO,J.L.ENGEL,J.ZHANG,M.J.CHEN,G.MANNING,J.E.DIXON JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF PTPMT1, A PHOSPHATASE JRNL TITL 2 REQUIRED FOR CARDIOLIPIN SYNTHESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 11860 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21730175 JRNL DOI 10.1073/PNAS.1109290108 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.3_473 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 11896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 44.7255 - 3.2470 0.99 2909 146 0.1684 0.1845 REMARK 3 2 3.2470 - 2.5773 0.99 2871 144 0.1751 0.2372 REMARK 3 3 2.5773 - 2.2515 0.98 2840 137 0.1752 0.2363 REMARK 3 4 2.2515 - 2.0500 0.94 2704 145 0.1819 0.2478 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 58.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.94380 REMARK 3 B22 (A**2) : -5.98250 REMARK 3 B33 (A**2) : -5.96130 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.60310 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 : 0.003 1303 REMARK 3 ANGLE : 0.772 1765 REMARK 3 CHIRALITY : 0.059 204 REMARK 3 PLANARITY : 0.003 216 REMARK 3 DIHEDRAL : 21.115 523 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 28.2624 -7.0844 7.1619 REMARK 3 T TENSOR REMARK 3 T11: 0.1151 T22: 0.0862 REMARK 3 T33: 0.0720 T12: -0.0111 REMARK 3 T13: 0.0097 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.3066 L22: 1.3861 REMARK 3 L33: 1.7510 L12: 0.6601 REMARK 3 L13: 0.9097 L23: 0.6783 REMARK 3 S TENSOR REMARK 3 S11: 0.1067 S12: -0.1279 S13: -0.0273 REMARK 3 S21: 0.2326 S22: -0.1079 S23: -0.0030 REMARK 3 S31: 0.2234 S32: -0.0020 S33: -0.0005 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 3RGQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11902 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 45.00950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.95700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.00950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.95700 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 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 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 273 LIES ON A SPECIAL POSITION. 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 O HOH A 270 O HOH A 271 2.17 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 PHE A 147 -45.21 82.90 REMARK 500 SER A 200 -151.54 -133.67 REMARK 500 SER A 205 -72.29 -133.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 5P5 A 300 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5P5 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RGO RELATED DB: PDB REMARK 900 APO STRUCTURE DBREF 3RGQ A 104 259 UNP Q66GT5 PTPM1_MOUSE 36 191 SEQADV 3RGQ SER A 200 UNP Q66GT5 CYS 132 ENGINEERED MUTATION SEQRES 1 A 156 ASP TRP TYR HIS ARG ILE ASP HIS THR VAL LEU LEU GLY SEQRES 2 A 156 ALA LEU PRO LEU LYS ASN MET THR ARG ARG LEU VAL LEU SEQRES 3 A 156 ASP GLU ASN VAL ARG GLY VAL ILE THR MET ASN GLU GLU SEQRES 4 A 156 TYR GLU THR ARG PHE LEU CYS ASN THR SER LYS GLU TRP SEQRES 5 A 156 LYS LYS ALA GLY VAL GLU GLN LEU ARG LEU SER THR VAL SEQRES 6 A 156 ASP MET THR GLY VAL PRO THR LEU ALA ASN LEU HIS LYS SEQRES 7 A 156 GLY VAL GLN PHE ALA LEU LYS TYR GLN ALA LEU GLY GLN SEQRES 8 A 156 CYS VAL TYR VAL HIS SER LYS ALA GLY ARG SER ARG SER SEQRES 9 A 156 ALA THR MET VAL ALA ALA TYR LEU ILE GLN VAL HIS ASN SEQRES 10 A 156 TRP SER PRO GLU GLU ALA ILE GLU ALA ILE ALA LYS ILE SEQRES 11 A 156 ARG SER HIS ILE SER ILE ARG PRO SER GLN LEU GLU VAL SEQRES 12 A 156 LEU LYS GLU PHE HIS LYS GLU ILE THR ALA ARG ALA ALA HET 5P5 A 300 31 HETNAM 5P5 (2R)-3-{[(S)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,4,6- HETNAM 2 5P5 TETRAHYDROXY-5-(PHOSPHONOOXY) HETNAM 3 5P5 CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYL HETNAM 4 5P5 DIBUTANOATE FORMUL 2 5P5 C17 H32 O16 P2 FORMUL 3 HOH *141(H2 O) HELIX 1 1 LEU A 120 ASN A 122 5 3 HELIX 2 2 MET A 123 ASP A 130 1 8 HELIX 3 3 GLU A 141 ARG A 146 1 6 HELIX 4 4 THR A 151 ALA A 158 1 8 HELIX 5 5 THR A 175 LEU A 192 1 18 HELIX 6 6 SER A 205 ASN A 220 1 16 HELIX 7 7 SER A 222 ARG A 234 1 13 HELIX 8 8 ARG A 240 ALA A 259 1 20 SHEET 1 A 5 TYR A 106 ARG A 108 0 SHEET 2 A 5 VAL A 113 GLY A 116 -1 O LEU A 115 N HIS A 107 SHEET 3 A 5 CYS A 195 HIS A 199 1 O VAL A 198 N LEU A 114 SHEET 4 A 5 VAL A 133 THR A 138 1 N ARG A 134 O CYS A 195 SHEET 5 A 5 GLU A 161 ARG A 164 1 O LEU A 163 N VAL A 136 SITE 1 AC1 13 HOH A 21 HOH A 83 TRP A 105 LEU A 118 SITE 2 AC1 13 MET A 170 SER A 200 LYS A 201 ALA A 202 SITE 3 AC1 13 GLY A 203 ARG A 204 SER A 205 ARG A 206 SITE 4 AC1 13 ARG A 240 CRYST1 90.019 67.914 32.088 90.00 96.56 90.00 C 1 2 1 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 0.011109 0.000000 0.001277 0.00000 SCALE2 0.000000 0.014725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031370 0.00000