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

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Basic information

Entry
Database: PDB / ID: 7dhf
TitleVibrio vulnificus Wzb in complex with benzylphosphonate
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / Vibrio / Wzb / low molecular weight protein tyrosine phosphatase (LMWPTP) / capsular polysaccharide
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
: / 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
Similarity search - Domain/homology
PHOSPHATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.211 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)65,6039
Polymers65,1314
Non-polymers4725
Water12,232679
1
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4703
Polymers16,2831
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,2831
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,2831
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,2831
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.972, 68.304, 132.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and ((resid 1 and (name N or name...
31(chain C and ((resid 1 and (name N or name...
41(chain D and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLY(chain A and ((resid 1 and (name N or name...AA14
12LEULEU(chain A and ((resid 1 and (name N or name...AA1 - 1464 - 149
13LEULEU(chain A and ((resid 1 and (name N or name...AA1 - 1464 - 149
14LEULEU(chain A and ((resid 1 and (name N or name...AA1 - 1464 - 149
15LEULEU(chain A and ((resid 1 and (name N or name...AA1 - 1464 - 149
16LEULEU(chain A and ((resid 1 and (name N or name...AA1 - 1464 - 149
21GLYGLY(chain B and ((resid 1 and (name N or name...BB14
22LEULEU(chain B and ((resid 1 and (name N or name...BB1 - 1464 - 149
23LEULEU(chain B and ((resid 1 and (name N or name...BB1 - 1464 - 149
24LEULEU(chain B and ((resid 1 and (name N or name...BB1 - 1464 - 149
25LEULEU(chain B and ((resid 1 and (name N or name...BB1 - 1464 - 149
26LEULEU(chain B and ((resid 1 and (name N or name...BB1 - 1464 - 149
31GLYGLY(chain C and ((resid 1 and (name N or name...CC14
32LEULEU(chain C and ((resid 1 and (name N or name...CC-2 - 1461 - 149
33LEULEU(chain C and ((resid 1 and (name N or name...CC-2 - 1461 - 149
34LEULEU(chain C and ((resid 1 and (name N or name...CC-2 - 1461 - 149
35LEULEU(chain C and ((resid 1 and (name N or name...CC-2 - 1461 - 149
36LEULEU(chain C and ((resid 1 and (name N or name...CC-2 - 1461 - 149
41GLYGLY(chain D and ((resid 1 and (name N or name...DD14
42PO4PO4(chain D and ((resid 1 and (name N or name...DD - I-2 - 2011
43PO4PO4(chain D and ((resid 1 and (name N or name...DD - I-2 - 2011
44PO4PO4(chain D and ((resid 1 and (name N or name...DD - I-2 - 2011
45PO4PO4(chain D and ((resid 1 and (name N or name...DD - I-2 - 2011
46PO4PO4(chain D and ((resid 1 and (name N or name...DD - I-2 - 2011

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Components

#1: Protein
Protein-tyrosine-phosphatase


Mass: 16282.812 Da / Num. of mol.: 4 / Mutation: C9A
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.13 %
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). The phosphate source was not defined, which was assumed to originate from the degradation or contamination of benzylphosphonate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.211→66.48 Å / Num. obs: 161631 / % possible obs: 95.7 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Rsym value: 0.078 / Net I/σ(I): 17.9
Reflection shellResolution: 1.211→1.232 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7689 / CC1/2: 0.933 / Rpim(I) all: 0.297 / Rrim(I) all: 1.118 / Rsym value: 1.077 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
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: 1.211→29.715 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 8104 5.02 %random selection
Rwork0.1434 153342 --
obs0.1447 161446 95.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.49 Å2 / Biso mean: 17.8791 Å2 / Biso min: 8.67 Å2
Refinement stepCycle: final / Resolution: 1.211→29.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 26 679 5227
Biso mean--19.35 29.87 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024693
X-RAY DIFFRACTIONf_angle_d0.5896360
X-RAY DIFFRACTIONf_chiral_restr0.058720
X-RAY DIFFRACTIONf_plane_restr0.003824
X-RAY DIFFRACTIONf_dihedral_angle_d17.3871795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2000X-RAY DIFFRACTION3.9TORSIONAL
12B2000X-RAY DIFFRACTION3.9TORSIONAL
13C2000X-RAY DIFFRACTION3.9TORSIONAL
14D2000X-RAY DIFFRACTION3.9TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2113-1.22510.27222660.2218486992
1.2251-1.23950.22492450.2011491092
1.2395-1.25460.2242720.2035489093
1.2546-1.27050.2272660.1974497893
1.2705-1.28720.21592310.1825490893
1.2872-1.30480.19492420.1855498894
1.3048-1.32350.22452600.1851498894
1.3235-1.34320.22592490.1809497294
1.3432-1.36420.21462810.1799496694
1.3642-1.38660.20383260.168499495
1.3866-1.41050.1762520.1546500895
1.4105-1.43610.17822500.1477501695
1.4361-1.46380.1472900.1395501195
1.4638-1.49360.18212700.144508295
1.4936-1.52610.16732940.1343507995
1.5261-1.56160.16312670.1313505496
1.5616-1.60070.16272770.1328509196
1.6007-1.64390.17182720.1334514396
1.6439-1.69230.17372580.1317512396
1.6923-1.74690.16472510.1334515696
1.7469-1.80930.15852490.1357518597
1.8093-1.88180.14342770.1336516997
1.8818-1.96740.16042600.133527197
1.9674-2.07110.1552790.1317520097
2.0711-2.20080.16442880.1312524898
2.2008-2.37070.14322630.1254529198
2.3707-2.60910.14572890.1343531798
2.6091-2.98640.16172870.1444535698
2.9864-3.76130.17092870.1385544399
3.7613-29.70.17573060.1505563699

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