[English] 日本語
Yorodumi
- PDB-5xch: Crystal structure of Wild type Vps29 complexed with Zn+2 from Ent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xch
TitleCrystal structure of Wild type Vps29 complexed with Zn+2 from Entamoeba histolytica
ComponentsVacuolar protein sorting-associated protein 29Vacuole
KeywordsPROTEIN TRANSPORT / Entamoeba histolytica / Vacuolar protein sorting 29 / Metallophosphatase fold / Calcineurin-like phosphoesterase superfamily domain
Function / homology
Function and homology information


retromer complex / retrograde transport, endosome to Golgi / intracellular protein transport / protein transport / endosome / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSrivastava, V.K. / Yadav, R. / Tomar, P. / Gourinath, S. / Datta, S.
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structural and thermodynamic characterization of metal binding in Vps29 from Entamoeba histolytica: implication in retromer function.
Authors: Srivastava, V.K. / Yadav, R. / Watanabe, N. / Tomar, P. / Mukherjee, M. / Gourinath, S. / Nakada-Tsukui, K. / Nozaki, T. / Datta, S.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0166
Polymers43,7542
Non-polymers2624
Water45025
1
A: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0083
Polymers21,8771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0083
Polymers21,8771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.310, 47.310, 148.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole


Mass: 21876.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HM-1:IMSS / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: vsp, EhVPS29, CL6EHI_025270, EHI_025270 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BI08
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % w/v PEG 20000, 20 % v/v PEGMME 550, 0.02 M of alcohol MIX, 0.1 M MES/Imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.45
ReflectionResolution: 2.85→40.9 Å / Num. obs: 8561 / % possible obs: 98 % / Redundancy: 11.2 % / Net I/σ(I): 21

-
Processing

Software
NameVersionClassification
iMOSFLMdata processing
SCALAdata reduction
PHASERphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCE

5xce


Resolution: 2.85→40.9 Å / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 33.53
RfactorNum. reflection% reflection
Rfree0.3068 411 4.8 %
Rwork0.2867 --
obs0.2879 8561 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 4 25 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052838
X-RAY DIFFRACTIONf_angle_d0.8423857
X-RAY DIFFRACTIONf_dihedral_angle_d19.7011684
X-RAY DIFFRACTIONf_chiral_restr0.054453
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.36411280.30972648X-RAY DIFFRACTION94
3.2744-4.10450.30751490.27932634X-RAY DIFFRACTION94
4.1045-13.16230.29161340.28132653X-RAY DIFFRACTION95

+
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