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- PDB-1huf: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE TYROSINE PHOSPH... -

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Basic information

Entry
Database: PDB / ID: 1huf
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE TYROSINE PHOSPHATASE YOPH FROM YERSINIA PESTIS.
ComponentsTYROSINE PHOSPHATASE YOPH
KeywordsHYDROLASE / helical bundle / beta hairpin
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / 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, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / 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, 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsEvdokimov, A.G. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the N-terminal domain of Yersinia pestis YopH at 2.0 A resolution.
Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Copeland, T.D. / Waugh, D.S.
History
DepositionJan 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE PHOSPHATASE YOPH


Theoretical massNumber of molelcules
Total (without water)15,0811
Polymers15,0811
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.063, 120.651, 49.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

21A-2034-

HOH

31A-2086-

HOH

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Components

#1: Protein TYROSINE PHOSPHATASE YOPH / EC 3.1.3.48 HYDROLASE / VIRULENCE PROTEIN


Mass: 15080.780 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YOPH / Plasmid: PKM904 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: O68720, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG4000, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %PEG60001reservoir
2100 mMTris-acetate1reservoiror sodium-bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 2000 / Details: Osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 9659 / Num. obs: 8860 / % possible obs: 83.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.01 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.045 / Net I/σ(I): 15.3
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.6 / Num. unique all: 711 / % possible all: 75.3
Reflection
*PLUS
Lowest resolution: 100 Å
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2→100 Å / Isotropic thermal model: isotropic one B factor per atom / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: One simulated annealing run (CNS) followed by conjugate-gradient least squares procedure. Data cutoff of 2 sigma is 8046 reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 773 8 %random
Rwork0.1892 ---
all0.2187 9659 --
obs0.1921 8860 97.4 %-
Solvent computationSolvent model: Babinet (SHELXL) / Bsol: 250 Å2 / ksol: 0.83 e/Å3
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 0 94 1030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.026
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
Software
*PLUS
Name: 'CNS, SHELXL-97' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg5.2
X-RAY DIFFRACTIONc_plane_restr0.003

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