10 20 30 40 50 60 70 80 5PNT - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 29-APR-98 5PNT
TITLE CRYSTAL STRUCTURE OF A HUMAN LOW MOLECULAR WEIGHT TITLE 2 PHOSPHOTYROSYL PHOSPHATASE. IMPLICATIONS FOR SUBSTRATE TITLE 3 SPECIFICITY
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW MOLECULAR WEIGHT PHOSPHOTYROSYL PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE; COMPND 5 EC: 3.1.3.2; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: CYTOSOL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11D
KEYWDS HYDROLASE, ACETYLATION, TYROSINE PHOSPHATASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.ZHANG,C.STAUFFACHER,D.LIN,R.VANETTEN
REVDAT 2 24-FEB-09 5PNT 1 VERSN REVDAT 1 14-OCT-98 5PNT 0
JRNL AUTH M.ZHANG,C.V.STAUFFACHER,D.LIN,R.L.VAN ETTEN JRNL TITL CRYSTAL STRUCTURE OF A HUMAN LOW MOLECULAR WEIGHT JRNL TITL 2 PHOSPHOTYROSYL PHOSPHATASE. IMPLICATIONS FOR JRNL TITL 3 SUBSTRATE SPECIFICITY. JRNL REF J.BIOL.CHEM. V. 273 21714 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9705307 JRNL DOI 10.1074/JBC.273.34.21714
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 8525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 355 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.02 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 0 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : 0 REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 GROUP 2 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 2 B-FACTOR (A**2) : NULL ; NULL REMARK 3 GROUP 3 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 3 B-FACTOR (A**2) : NULL ; NULL REMARK 3 GROUP 4 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 4 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 5PNT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 10.000 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : 0.07700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : 0.24500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: PDB ENTRY 1PNT REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 30% REMARK 280 PEGMME 5000, 200 MM AMMONIUM SULFATE, 100 MM MES, PH 6.5
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 17.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.30000 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 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 CYS A 17 -60.98 -102.41 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 MES A 0
DBREF 5PNT A 1 157 UNP P24666 PPAC_HUMAN 1 157
SEQRES 1 A 157 ALA GLU GLN ALA THR LYS SER VAL LEU PHE VAL CYS LEU SEQRES 2 A 157 GLY ASN ILE CYS ARG SER PRO ILE ALA GLU ALA VAL PHE SEQRES 3 A 157 ARG LYS LEU VAL THR ASP GLN ASN ILE SER GLU ASN TRP SEQRES 4 A 157 ARG VAL ASP SER ALA ALA THR SER GLY TYR GLU ILE GLY SEQRES 5 A 157 ASN PRO PRO ASP TYR ARG GLY GLN SER CYS MET LYS ARG SEQRES 6 A 157 HIS GLY ILE PRO MET SER HIS VAL ALA ARG GLN ILE THR SEQRES 7 A 157 LYS GLU ASP PHE ALA THR PHE ASP TYR ILE LEU CYS MET SEQRES 8 A 157 ASP GLU SER ASN LEU ARG ASP LEU ASN ARG LYS SER ASN SEQRES 9 A 157 GLN VAL LYS THR CYS LYS ALA LYS ILE GLU LEU LEU GLY SEQRES 10 A 157 SER TYR ASP PRO GLN LYS GLN LEU ILE ILE GLU ASP PRO SEQRES 11 A 157 TYR TYR GLY ASN ASP SER ASP PHE GLU THR VAL TYR GLN SEQRES 12 A 157 GLN CYS VAL ARG CYS CYS ARG ALA PHE LEU GLU LYS ALA SEQRES 13 A 157 HIS
HET MES A 0 12
HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *82(H2 O)
HELIX 1 1 SER A 19 ASP A 32 1 14 HELIX 2 2 SER A 36 ASN A 38 5 3 HELIX 3 3 TYR A 57 HIS A 66 1 10 HELIX 4 4 GLU A 80 THR A 84 5 5 HELIX 5 5 GLU A 93 GLN A 105 1 13 HELIX 6 6 LEU A 116 TYR A 119 5 4 HELIX 7 7 ASP A 135 LYS A 155 1 21
SHEET 1 A 4 TRP A 39 ALA A 45 0 SHEET 2 A 4 LYS A 6 CYS A 12 1 N LYS A 6 O ARG A 40 SHEET 3 A 4 TYR A 87 CYS A 90 1 N TYR A 87 O LEU A 9 SHEET 4 A 4 LYS A 112 LEU A 115 1 N LYS A 112 O ILE A 88
SITE 1 AC1 12 CYS A 12 LEU A 13 GLY A 14 ASN A 15 SITE 2 AC1 12 ILE A 16 CYS A 17 ARG A 18 GLU A 50 SITE 3 AC1 12 ARG A 97 ASP A 129 TYR A 131 HOH A 161
CRYST1 34.100 56.600 97.300 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 0.029326 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017668 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010277 0.00000