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- PDB-1ypt: CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5... -

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Basic information

Entry
Database: PDB / ID: 1ypt
TitleCRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE
ComponentsPROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsStuckey, J.A. / Schubert, H.L. / Fauman, E.B. / Zhang, Z.-Y. / Dixon, J.E. / Saper, M.A.
Citation
Journal: Nature / Year: 1994
Title: Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate.
Authors: Stuckey, J.A. / Schubert, H.L. / Fauman, E.B. / Zhang, Z.Y. / Dixon, J.E. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Expression, Purification, and Physicochemical Characterization of a Recombinant Yersinia Protein Tyrosine Phosphatase
Authors: Zhang, Z.-Y. / Clemens, J.C. / Schubert, H.L. / Stuckey, J.A. / Fischer, M.W.F. / Hume, D.M. / Saper, M.A. / Dixon, J.E.
History
DepositionSep 16, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)
B: PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)


Theoretical massNumber of molelcules
Total (without water)66,8452
Polymers66,8452
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.530, 71.530, 107.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9922, 0.091653, 0.08449), (0.088672, -0.995321, 0.038391), (0.087614, -0.0306, -0.995684)
Vector: -5.652, 39.558, 93.757)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 191 - A 468 B 191 - B 468 .223 A 178.02 DEGREE ROTATION ABOUT THE X AXIS OF THE CRYSTAL THAT RELATES MOLECULE A TO MOLECULE B. THE RMSD (EXCLUDING 4 FLEXIBLE LOOPS) BETWEEN MOLECULE A AND MOLECULE B IS 0.196. THE RMSD USING ALL ATOMS IS 0.523.

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE YERSINIA (CATALYTIC DOMAIN)


Mass: 33422.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YOP51 / Plasmid: PT7-7 GENE: YOP51 / Gene (production host): YOP51 / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growDetails: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 22 DEGREES CELSIUS, IN A SOLUTION OF 10 - 16% POLYETHYLENE GLYCOL, 5% 2-METHYL-2,4-PENTANEDIOL, 0.1% B-MERCAPTOETHANOL, ...Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 22 DEGREES CELSIUS, IN A SOLUTION OF 10 - 16% POLYETHYLENE GLYCOL, 5% 2-METHYL-2,4-PENTANEDIOL, 0.1% B-MERCAPTOETHANOL, AND 1MM IMIDAZOLE, PH 7.2. SOURCE ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS EXPRESSED FOR THIS PARTICULAR EXPERIMENT. THE 235 CYS TO ARG MUTATION WAS UNINTENTIONAL AND MOST LIKELY THE RESULT OF USING PCR TO CONSTRUCT THE PLASMID (SEE REFERENCE REMARK 1).
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
20.1 %beta-mercaptoethanol1drop
31 mMimidazole1drop
410-15 %PEG15001drop
530 %PEG15001reservoir
6MPD1dropsmall amount

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Data collection

ReflectionNum. obs: 19476 / % possible obs: 91 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.222 --
Rwork0.168 --
obs0.168 17095 84 %
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 0 65 4355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.93
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.81
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.168 / Rfactor Rfree: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.93
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.25

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