HEADER HYDROLASE 23-NOV-99 1DG9 TITLE CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE COMPLEXED WITH TITLE 2 HEPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.3.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: HEART; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS PTPASE, HEPES COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHANG,M.ZHOU,R.L.VAN ETTEN,C.V.STAUFFACHER REVDAT 5 07-FEB-24 1DG9 1 REMARK REVDAT 4 04-OCT-17 1DG9 1 REMARK REVDAT 3 24-FEB-09 1DG9 1 VERSN REVDAT 2 15-MAR-05 1DG9 1 REMARK REVDAT 1 08-DEC-99 1DG9 0 JRNL AUTH M.ZHANG,M.ZHOU,R.L.VAN ETTEN,C.V.STAUFFACHER JRNL TITL CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT JRNL TITL 2 PHOSPHOTYROSYL PHOSPHATASE COMPLEXED WITH THE TRANSITION JRNL TITL 3 STATE ANALOG VANADATE. JRNL REF BIOCHEMISTRY V. 36 15 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 8993313 JRNL DOI 10.1021/BI961804N REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11869 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.340 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71205 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4K, 10% 2-PROPANOL, 100MM REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION 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 47.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.70000 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 93 CD GLU A 93 OE2 0.068 REMARK 500 GLU A 154 CD GLU A 154 OE2 0.086 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 12 N - CA - CB ANGL. DEV. = 9.3 DEGREES REMARK 500 ASP A 37 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 37 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 42 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP A 56 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 56 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 120 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 147 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 147 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES 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 GLN A 3 -148.25 -164.54 REMARK 500 ASN A 108 54.13 -105.49 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 EPE A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PNT RELATED DB: PDB REMARK 900 1PNT CONTAINS THE SAME PROTEIN COMPLEXED WITH PO4 REMARK 900 RELATED ID: 2PNT RELATED DB: PDB REMARK 900 THIS IS THE ID CODE USED IN THE PRIMARY CITATION. DBREF 1DG9 A 1 157 UNP P11064 PPAC_BOVIN 1 157 SEQRES 1 A 157 ALA GLU GLN VAL 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 ASP ASN TRP SEQRES 4 A 157 VAL ILE ASP SER GLY ALA VAL SER ASP TRP ASN VAL GLY SEQRES 5 A 157 ARG SER PRO ASP PRO ARG ALA VAL SER CYS LEU ARG ASN SEQRES 6 A 157 HIS GLY ILE ASN THR ALA HIS LYS ALA ARG GLN VAL THR SEQRES 7 A 157 LYS GLU ASP PHE VAL 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 ASN CYS ARG 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 ALA ASP PHE GLU THR VAL TYR GLN SEQRES 12 A 157 GLN CYS VAL ARG CYS CYS ARG ALA PHE LEU GLU LYS VAL SEQRES 13 A 157 ARG HET EPE A 201 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S HELIX 1 1 CYS A 17 GLN A 33 1 17 HELIX 2 2 ILE A 35 ASP A 37 5 3 HELIX 3 3 ASP A 56 HIS A 66 1 11 HELIX 4 4 GLU A 80 PHE A 85 1 6 HELIX 5 5 ASP A 92 ASN A 104 1 13 HELIX 6 6 GLY A 117 ASP A 120 5 4 HELIX 7 7 ASN A 134 ARG A 157 1 24 SHEET 1 A 4 TRP A 39 ALA A 45 0 SHEET 2 A 4 LYS A 6 CYS A 12 1 O LYS A 6 N VAL A 40 SHEET 3 A 4 TYR A 87 CYS A 90 1 O TYR A 87 N LEU A 9 SHEET 4 A 4 LYS A 112 LEU A 115 1 O LYS A 112 N ILE A 88 SITE 1 AC1 10 CYS A 12 LEU A 13 GLY A 14 ASN A 15 SITE 2 AC1 10 ILE A 16 CYS A 17 ARG A 18 ASP A 129 SITE 3 AC1 10 TYR A 131 TYR A 132 CRYST1 95.300 43.400 41.200 90.00 113.40 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 0.010493 0.000000 0.004541 0.00000 SCALE2 0.000000 0.023041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026447 0.00000