[English] 日本語
Yorodumi
- PDB-4gsw: Crystal structure of ubiquitin from Entamoeba histolytica to 2.15... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gsw
TitleCrystal structure of ubiquitin from Entamoeba histolytica to 2.15 Angstrom
ComponentsUbiquitin
KeywordsPROTEIN BINDING / ubiquitin / ubiquitin-like modifier / ubiquitin fold / post-translational modification / EhUbc5 / EhUba1 / ubiquitination / isopeptide bond
Function / homology
Function and homology information


modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica.
Authors: Bosch, D.E. / Siderovski, D.P.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1574
Polymers17,9652
Non-polymers1922
Water79344
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1743
Polymers8,9821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9821
Polymers8,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.631, 49.865, 76.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin / Ubiquitin / putative


Mass: 8982.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote)
Gene: EhUBI1, EHI_083270, EHI_083410, EHI_156660, EHI_178340
Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / References: UniProt: C4M760
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR ...Details: EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 8593 / Num. obs: 8430 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.6
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.1 / Num. unique all: 210 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UBQ

1ubq


Resolution: 2.15→34.513 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 840 10.03 %RANDOM
Rwork0.1932 ---
obs0.1994 8379 97.53 %-
all-8591 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→34.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 10 44 1219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141192
X-RAY DIFFRACTIONf_angle_d1.4931606
X-RAY DIFFRACTIONf_dihedral_angle_d16.107470
X-RAY DIFFRACTIONf_chiral_restr0.094191
X-RAY DIFFRACTIONf_plane_restr0.007204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.15-2.27720.35051290.26581154115492
2.2772-2.4530.34711350.2456121397
2.453-2.69970.33611410.2415126099
2.6997-3.09020.2711410.2206127699
3.0902-3.89240.26421450.1768129399
3.8924-34.51760.1931490.1598134398
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)
18.88254.2839-6.42947.5101-5.52087.7505-0.13630.0645-0.1283-0.5750.09030.49810.28890.11230.00820.3596-0.026-0.01210.3096-0.08560.4316-2.9252-17.067216.8572
28.73584.4651-1.00123.6026-2.17924.21650.1084-0.0855-0.0624-0.4293-0.1908-0.37670.0558-0.05220.04360.33240.0713-0.02590.2434-0.02330.4811-5.1492-8.057314.249
36.8637-5.00760.93687.13490.04183.50570.1044-0.21530.9020.453-0.01210.0763-0.19470.15020.00790.4440.0032-0.02670.2985-0.00850.465-5.512-7.009525.2201
46.0129-0.3649-3.39474.8498-0.0772.1587-0.0693-0.3594-0.0825-0.0779-0.1956-0.03860.06910.24660.25270.24230.0302-0.12380.29140.00470.35441.2656-9.278621.362
59.33616.6156-2.88015.9387-2.04633.07990.31540.1665-0.53050.7282-0.0346-1.32570.29010.3948-0.49720.4475-0.0134-0.08070.4096-0.030.395-11.35663.61421.4181
64.43232.33951.56562.1663.4679.09850.1158-0.07230.1625-0.1913-0.11210.0043-0.10420.03050.06830.29250.03410.01610.2180.02650.4959-10.10492.237812.3134
74.18181.6119-1.32735.30561.80394.8203-0.10590.0158-0.1921-0.2086-0.0002-0.03430.2476-0.76750.04390.34010.0264-0.09460.42270.07910.4536-22.1508-0.0988.1131
83.6481-0.3188-0.16834.82383.91093.26130.22740.2805-0.2308-0.25130.0457-0.7924-0.2597-0.7043-0.02810.40430.03070.01490.37960.08290.5466-17.04726.37415.4694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:18)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:55)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 56:75)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 4:23)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 24:44)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 45:64)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 65:76)

+
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://pdbjlvh1.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