[English] 日本語
Yorodumi
- PDB-7dhe: Vibrio vulnificus Wzb in complex with benzylphosphonate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dhe
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, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning 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
benzylphosphonic acid / protein-tyrosine-phosphatase
Similarity search - Component
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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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).

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more