10 20 30 40 50 60 70 80 2DXP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 29-AUG-06 2DXP
TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF THE ARCHAEAL SULFOLOBUS TITLE 2 PTP-FOLD PHOSPHATASE WITH PHOSPHOPEPTIDES A-(P)Y-R
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SULFOLOBUS SOLFATARICUS PROTEIN TYROSINE COMPND 3 PHOSPHATASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: SSOPTP; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: A(PTR)R; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SYNTHETIC PEPTIDE
KEYWDS PTP DOMAIN, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.M.CHU,A.H.J.WANG
REVDAT 2 24-FEB-09 2DXP 1 VERSN REVDAT 1 13-MAR-07 2DXP 0
JRNL AUTH H.M.CHU,A.H.J.WANG JRNL TITL ENZYME-SUBSTRATE INTERACTIONS REVEALED BY THE JRNL TITL 2 CRYSTAL STRUCTURES OF THE ARCHAEAL SULFOLOBUS JRNL TITL 3 PTP-FOLD PHOSPHATASE AND ITS PHOSPHOPEPTIDE JRNL TITL 4 COMPLEXES JRNL REF PROTEINS V. 66 996 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17173287 JRNL DOI 10.1002/PROT.21262
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 9678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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 : 1310 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL 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 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2DXP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB025972.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9678 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.67600 REMARK 200 R SYM FOR SHELL (I) : 0.57800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1OHE REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K
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 40.76950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.11600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.76950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.11600 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: 420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A5288 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 SER A 159 REMARK 465 ASN A 160 REMARK 465 SER A 161
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 ARG A 6 102.98 -19.65 REMARK 500 SER A 96 -138.74 -119.31 REMARK 500 VAL A 134 104.20 80.12 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B5278 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH B5283 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH A5244 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A5281 DISTANCE = 6.36 ANGSTROMS
REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 5288
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I6I RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 2I6J RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH PHOSPHATE ION REMARK 900 RELATED ID: 2I6M RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH TUNGSTATE REMARK 900 RELATED ID: 2I6O RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH PHOSPHOPEPTIDES N-G-(P)Y-K-N REMARK 900 RELATED ID: 2I6P RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH PNPP
DBREF 2DXP A 1 161 UNP Q97VZ7 Q97VZ7_SULSO 1 161 DBREF 2DXP B 170 172 PDB 2DXP 2DXP 170 172
SEQADV 2DXP SER A 96 UNP Q97VZ7 CYS 96 ENGINEERED
SEQRES 1 A 161 MET TYR TRP VAL ARG ARG LYS THR ILE GLY GLY SER GLY SEQRES 2 A 161 LEU PRO TYR THR GLU ASN GLU ILE LEU GLU TRP ARG LYS SEQRES 3 A 161 GLU GLY VAL LYS ARG VAL LEU VAL LEU PRO GLU ASP TRP SEQRES 4 A 161 GLU ILE GLU GLU SER TRP GLY ASP LYS ASP TYR TYR LEU SEQRES 5 A 161 SER ILE LEU LYS LYS ASN GLY LEU GLN PRO LEU HIS ILE SEQRES 6 A 161 PRO ILE PRO ASP GLY GLY VAL PRO SER ASP SER GLN PHE SEQRES 7 A 161 LEU THR ILE MET LYS TRP LEU LEU SER GLU LYS GLU GLY SEQRES 8 A 161 ASN LEU VAL HIS SER VAL GLY GLY ILE GLY ARG THR GLY SEQRES 9 A 161 THR ILE LEU ALA SER TYR LEU ILE LEU THR GLU GLY LEU SEQRES 10 A 161 GLU VAL GLU SER ALA ILE ASP GLU VAL ARG LEU VAL ARG SEQRES 11 A 161 PRO GLY ALA VAL GLN THR TYR GLU GLN GLU MET PHE LEU SEQRES 12 A 161 LEU ARG VAL GLU GLY MET ARG LYS SER TRP LEU LYS ASN SEQRES 13 A 161 ILE TYR SER ASN SER SEQRES 1 B 3 ALA PTR ARG
MODRES 2DXP PTR B 171 TYR O-PHOSPHOTYROSINE
HET PTR B 171 16
HETNAM PTR O-PHOSPHOTYROSINE
HETSYN PTR PHOSPHONOTYROSINE
FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *88(H2 O)
HELIX 1 1 THR A 17 GLY A 28 1 12 HELIX 2 2 GLU A 37 GLY A 46 1 10 HELIX 3 3 ASP A 47 ASN A 58 1 12 HELIX 4 4 SER A 74 GLU A 88 1 15 HELIX 5 5 ILE A 100 GLU A 115 1 16 HELIX 6 6 GLU A 118 LEU A 128 1 11 HELIX 7 7 THR A 136 MET A 149 1 14 HELIX 8 8 MET A 149 TYR A 158 1 10
SHEET 1 A 5 TYR A 2 ARG A 5 0 SHEET 2 A 5 ILE A 9 SER A 12 -1 O ILE A 9 N VAL A 4 SHEET 3 A 5 ASN A 92 HIS A 95 1 O ASN A 92 N GLY A 10 SHEET 4 A 5 ARG A 31 VAL A 34 1 N LEU A 33 O LEU A 93 SHEET 5 A 5 GLN A 61 HIS A 64 1 O LEU A 63 N VAL A 34
LINK C ALA B 170 N PTR B 171 1555 1555 1.33 LINK C PTR B 171 N ARG B 172 1555 1555 1.33
CRYST1 81.539 58.232 36.475 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 0.012264 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017173 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027416 0.00000