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- PDB-7dhe: Vibrio vulnificus Wzb in complex with benzylphosphonate -

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Basic information

Entry
Database: PDB / ID: 7dhe
TitleVibrio vulnificus Wzb in complex with benzylphosphonate
ComponentsProtein-tyrosine-phosphataseProtein tyrosine phosphatase
KeywordsHYDROLASE / Vibrio / Wzb / low molecular weight protein tyrosine phosphatase (LMWPTP) / capsular polysaccharide
Function / homologyProtein-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 / benzylphosphonic acid / protein-tyrosine-phosphatase
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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
C: Protein-tyrosine-phosphatase
D: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9488
Polymers65,2604
Non-polymers6884
Water0
1
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4872
Polymers16,3151
Non-polymers1721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4872
Polymers16,3151
Non-polymers1721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4872
Polymers16,3151
Non-polymers1721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4872
Polymers16,3151
Non-polymers1721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.110, 51.010, 68.590
Angle α, β, γ (deg.)101.850, 95.560, 103.790
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein-tyrosine-phosphatase / Protein tyrosine phosphatase


Mass: 16314.879 Da / Num. of mol.: 4
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-B85 / benzylphosphonic acid


Mass: 172.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9O3P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Complex crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml protein in the buffer 10 mM HEPES, 30 mM benzylphophonate, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1.5 ul of ...Details: Complex crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml protein in the buffer 10 mM HEPES, 30 mM benzylphophonate, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1.5 ul of reservoir solution (100 mM HEPES pH 7.0, 25% (w/v) PEG3350).

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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: 2.785→48.14 Å / Num. obs: 13744 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Rsym value: 0.047 / Net I/σ(I): 16.4
Reflection shellResolution: 2.785→2.833 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 689 / CC1/2: 0.811 / Rpim(I) all: 0.345 / Rrim(I) all: 0.666 / Rsym value: 0.568 / % possible all: 97.9

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Processing

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

2wmy


Resolution: 2.79→48.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.347
RfactorNum. reflection% reflectionSelection details
Rfree0.226 690 5.05 %RANDOM
Rwork0.186 ---
obs0.188 13670 97.9 %-
Displacement parametersBiso max: 192.39 Å2 / Biso mean: 91.92 Å2 / Biso min: 48.82 Å2
Baniso -1Baniso -2Baniso -3
1--10.3689 Å2-5.244 Å22.7227 Å2
2--3.3881 Å29.8264 Å2
3---6.9808 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.79→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 44 0 4544
Biso mean--106.28 --
Num. residues----585
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1648SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4618HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion609SEMIHARMONIC5
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_contact5444SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4618HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6238HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion22.08
LS refinement shellResolution: 2.79→3.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.275 126 4.45 %
Rwork0.244 2707 -
all0.245 2833 -
obs--98.2 %
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)
16.7503-2.31440.84494.90081.23484.15010.0983-0.31540.23990.3980.0304-0.00010.09440.0176-0.1287-0.23930.00880.1008-0.1050.0301-0.148248.99494.8218-10.5047
28.8563-1.85120.81724.8328-0.41776.70570.71971.81190.5137-0.5176-0.62210.39390.30980.6208-0.0976-0.31850.2777-0.04560.16370.0342-0.257429.65198.898-38.2899
35.9346-3.3473-1.34958.36041.10933.5091-0.8863-0.8729-0.12341.06850.5137-0.6806-0.22470.05930.3727-0.03780.2663-0.1786-0.0448-0.066-0.194627.88920.65847.0857
45.8483-4.6756-1.53846.29831.32323.3020.27080.40260.382-0.6909-0.1768-0.42060.1559-0.3607-0.0939-0.2083-0.00570.0026-0.22640.0446-0.077915.887832.3129-22.7047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|146 }A1 - 146
2X-RAY DIFFRACTION2{ B|0 - B|146 }B0 - 146
3X-RAY DIFFRACTION3{ C|1 - C|146 }C1 - 146
4X-RAY DIFFRACTION4{ D|1 - D|146 }D1 - 146

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