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- PDB-7dhd: Vibrio vulnificus Wzb -

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Basic information

Entry
Database: PDB / ID: 7dhd
TitleVibrio vulnificus Wzb
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / Vibrio / Wzb / low molecular weight protein tyrosine phosphatase (LMWPTP) / capsular polysaccharide
Function / homology: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMa, Q. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences100 talent program China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Wzb of Vibrio vulnificus represents a new group of low-molecular-weight protein tyrosine phosphatases with a unique insertion in the W-loop.
Authors: Wang, X. / Ma, Q.
History
DepositionNov 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine-phosphatase
B: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7014
Polymers32,6302
Non-polymers712
Water4,864270
1
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3502
Polymers16,3151
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7630 Å2
MethodPISA
2
B: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3502
Polymers16,3151
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.315, 48.741, 117.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein-tyrosine-phosphatase


Mass: 16314.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: wzb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: E5F0S0, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Free VvWzb crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT) and 1.5 ul of reservoir solution (100 mM ...Details: Free VvWzb crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT) and 1.5 ul of reservoir solution (100 mM HEPES pH7.5, 200 mM NaCl, 31% (w/v) PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.71→58.66 Å / Num. obs: 29957 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Rsym value: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 1.711→1.74 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1506 / CC1/2: 0.788 / Rpim(I) all: 0.343 / Rrim(I) all: 1.238 / Rsym value: 1.188 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSJan 31, 2020 (BUILT 20200417)data reduction
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WMY

2wmy


Resolution: 1.71→58.66 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1437 4.8 %RANDOM
Rwork0.199 ---
obs0.2 29954 99.4 %-
Displacement parametersBiso max: 111.09 Å2 / Biso mean: 32.58 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-7.5225 Å20 Å20 Å2
2--5.967 Å20 Å2
3----13.4895 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.71→58.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 2 270 2544
Biso mean--28.08 36.38 -
Num. residues----296
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it2314HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2857SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2314HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3125HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion17.95
LS refinement shellResolution: 1.71→1.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.322 134 4.71 %
Rwork0.271 2714 -
all0.274 2848 -
obs--98.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4104-0.2942-0.26761.65420.14230.68040.06230.1080.1718-0.1085-0.0444-0.042-0.0130.0215-0.0179-0.0550.01380.0005-0.03580.0501-0.0469-9.03853.786-7.6283
21.44180.00870.21221.20310.28311.42110.002-0.23850.1330.08110.00930.0114-0.0547-0.3604-0.0113-0.06290.0218-0.00340.05880.0277-0.1595-10.8047-7.512217.5161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-1 - A|146 }A-1 - 146
2X-RAY DIFFRACTION2{ B|-1 - B|146 }B-1 - 146

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