HEADER HYDROLASE 08-APR-11 3RGO
TITLE CRYSTAL STRUCTURE OF PTPMT1
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
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 3RGO 1 REMARK
REVDAT 4 08-NOV-17 3RGO 1 REMARK
REVDAT 3 03-AUG-11 3RGO 1 JRNL
REVDAT 2 20-JUL-11 3RGO 1 JRNL
REVDAT 1 06-JUL-11 3RGO 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. 1.93 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.5_2
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) : 1.93
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.75
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 12667
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.228
REMARK 3 R VALUE (WORKING SET) : 0.227
REMARK 3 FREE R VALUE : 0.243
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880
REMARK 3 FREE R VALUE TEST SET COUNT : 618
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 34.7550 - 3.0594 1.00 3206 160 0.2231 0.2196
REMARK 3 2 3.0594 - 2.4286 1.00 3007 146 0.2245 0.2703
REMARK 3 3 2.4286 - 2.1216 1.00 2957 155 0.2304 0.2830
REMARK 3 4 2.1216 - 1.9280 0.99 2879 157 0.2499 0.3108
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 : 0.34
REMARK 3 B_SOL : 46.55
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250
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) : 51.77
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.73050
REMARK 3 B22 (A**2) : 2.73050
REMARK 3 B33 (A**2) : -5.46100
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 : 0.004 1289
REMARK 3 ANGLE : 0.776 1743
REMARK 3 CHIRALITY : 0.055 198
REMARK 3 PLANARITY : 0.003 217
REMARK 3 DIHEDRAL : 16.639 473
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): 13.1083 -1.3176 -15.3095
REMARK 3 T TENSOR
REMARK 3 T11: 0.3722 T22: 0.1683
REMARK 3 T33: 0.3159 T12: 0.0068
REMARK 3 T13: 0.1559 T23: -0.0307
REMARK 3 L TENSOR
REMARK 3 L11: 2.1035 L22: 2.0857
REMARK 3 L33: 4.5529 L12: -0.0219
REMARK 3 L13: 0.1938 L23: 0.5842
REMARK 3 S TENSOR
REMARK 3 S11: 0.0463 S12: -0.0883 S13: 0.0804
REMARK 3 S21: 0.0657 S22: -0.0658 S23: -0.1551
REMARK 3 S31: 0.0337 S32: 0.1107 S33: -0.0069
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 3RGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-11.
REMARK 100 THE DEPOSITION ID IS D_1000064908.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-DEC-09; 29-JAN-10
REMARK 200 TEMPERATURE (KELVIN) : 100; 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y; Y
REMARK 200 RADIATION SOURCE : ALS; ALS
REMARK 200 BEAMLINE : 8.2.1; 8.2.1
REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 0.9798, 0.9800, 0.9573
REMARK 200 MONOCHROMATOR : NULL; NULL
REMARK 200 OPTICS : NULL; NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD; CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM
REMARK 200 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 : 12762
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.928
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 (%) : 99.9
REMARK 200 DATA REDUNDANCY : 12.70
REMARK 200 R MERGE (I) : 0.05100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 13.20
REMARK 200 R MERGE FOR SHELL (I) : 0.70500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.29
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, BIS-TRIS, (NH4)2SO4, PH
REMARK 280 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 115.01200
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.22650
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.22650
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 172.51800
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.22650
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.22650
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.50600
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.22650
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.22650
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 172.51800
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.22650
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.22650
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 57.50600
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 115.01200
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 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 71 132.33 -34.94
REMARK 500 MET A 72 -5.41 72.17
REMARK 500 CYS A 102 -103.55 -124.87
REMARK 500 LYS A 103 -68.31 -103.81
REMARK 500 SER A 107 -75.83 -135.74
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 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3RGQ RELATED DB: PDB
DBREF 3RGO A 7 163 UNP Q66GT5 PTPM1_MOUSE 37 193
SEQRES 1 A 157 TRP TYR HIS ARG ILE ASP HIS THR VAL LEU LEU GLY ALA
SEQRES 2 A 157 LEU PRO LEU LYS ASN MET THR ARG ARG LEU VAL LEU ASP
SEQRES 3 A 157 GLU ASN VAL ARG GLY VAL ILE THR MET ASN GLU GLU TYR
SEQRES 4 A 157 GLU THR ARG PHE LEU CYS ASN THR SER LYS GLU TRP LYS
SEQRES 5 A 157 LYS ALA GLY VAL GLU GLN LEU ARG LEU SER THR VAL ASP
SEQRES 6 A 157 MET THR GLY VAL PRO THR LEU ALA ASN LEU HIS LYS GLY
SEQRES 7 A 157 VAL GLN PHE ALA LEU LYS TYR GLN ALA LEU GLY GLN CYS
SEQRES 8 A 157 VAL TYR VAL HIS CYS LYS ALA GLY ARG SER ARG SER ALA
SEQRES 9 A 157 THR MET VAL ALA ALA TYR LEU ILE GLN VAL HIS ASN TRP
SEQRES 10 A 157 SER PRO GLU GLU ALA ILE GLU ALA ILE ALA LYS ILE ARG
SEQRES 11 A 157 SER HIS ILE SER ILE ARG PRO SER GLN LEU GLU VAL LEU
SEQRES 12 A 157 LYS GLU PHE HIS LYS GLU ILE THR ALA ARG ALA ALA LYS
SEQRES 13 A 157 ASN
HET SO4 A 1 5
HET SO4 A 2 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 2(O4 S 2-)
FORMUL 4 HOH *48(H2 O)
HELIX 1 1 LEU A 22 ASN A 24 5 3
HELIX 2 2 MET A 25 GLU A 33 1 9
HELIX 3 3 THR A 53 ALA A 60 1 8
HELIX 4 4 THR A 77 GLY A 95 1 19
HELIX 5 5 SER A 107 ASN A 122 1 16
HELIX 6 6 SER A 124 ARG A 136 1 13
HELIX 7 7 ARG A 142 ALA A 161 1 20
SHEET 1 A 5 TYR A 8 ARG A 10 0
SHEET 2 A 5 VAL A 15 GLY A 18 -1 O LEU A 17 N HIS A 9
SHEET 3 A 5 CYS A 97 HIS A 101 1 O VAL A 100 N LEU A 16
SHEET 4 A 5 VAL A 35 MET A 41 1 N ARG A 36 O CYS A 97
SHEET 5 A 5 GLU A 63 LEU A 67 1 O LEU A 65 N VAL A 38
SITE 1 AC1 9 HOH A 5 CYS A 102 LYS A 103 ALA A 104
SITE 2 AC1 9 GLY A 105 ARG A 106 SER A 107 ARG A 108
SITE 3 AC1 9 SER A 109
SITE 1 AC2 8 ASN A 42 THR A 69 VAL A 70 ASP A 71
SITE 2 AC2 8 MET A 72 THR A 73 GLY A 74 ARG A 108
CRYST1 36.453 36.453 230.024 90.00 90.00 90.00 P 43 21 2 8
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 0.027433 0.000000 0.000000 0.00000
SCALE2 0.000000 0.027433 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004347 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
