[English] 日本語
Yorodumi
- PDB-6hb2: Structure of Hgh1, crystal form I, Selenomethionine derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hb2
TitleStructure of Hgh1, crystal form I, Selenomethionine derivative
ComponentsProtein HGH1
KeywordsCHAPERONE / solenoid protein / Armadillo repeat
Function / homology
Function and homology information


translation elongation factor binding / : / nucleus / cytoplasm
Similarity search - Function
Protein HGH1 N-terminal / Protein HGH1 C-terminal / Protein Hgh1 / Domain of unknown function (DUF383) / Domain of unknown function (DUF384) / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMoenkemeyer, L. / Klaips, C.L. / Balchin, D. / Koerner, R. / Hartl, F.U. / Bracher, A.
CitationJournal: Mol.Cell / Year: 2019
Title: Chaperone Function of Hgh1 in the Biogenesis of Eukaryotic Elongation Factor 2.
Authors: Monkemeyer, L. / Klaips, C.L. / Balchin, D. / Korner, R. / Hartl, F.U. / Bracher, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein HGH1
B: Protein HGH1
C: Protein HGH1
D: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,4775
Polymers169,4424
Non-polymers351
Water1,29772
1
A: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)42,3601
Polymers42,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)42,3601
Polymers42,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)42,3601
Polymers42,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3962
Polymers42,3601
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.415, 87.212, 88.682
Angle α, β, γ (deg.)118.070, 105.970, 99.540
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Protein HGH1 / HMG1/2 protein homolog


Mass: 42360.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HGH1, YGR187C, G7538 / Plasmid: pProEX-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: P48362
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.86 % / Mosaicity: 0.12 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG-3350, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 20 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.7→44.75 Å / Num. obs: 52277 / % possible obs: 99.1 % / Redundancy: 13.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.053 / Rrim(I) all: 0.201 / Net I/σ(I): 13.3 / Num. measured all: 722320 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.7811.61.52843310.7740.4391.59293.9
11.12-44.7513.70.1067350.9970.0290.1197.7

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.612 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.88 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2142 5301 5.09 %
Rwork0.1902 --
obs0.1915 104053 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.98 Å2 / Biso mean: 68.6373 Å2 / Biso min: 24.22 Å2
Refinement stepCycle: final / Resolution: 2.7→29.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11447 0 1 72 11520
Biso mean--51.63 53.2 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411643
X-RAY DIFFRACTIONf_angle_d0.75915714
X-RAY DIFFRACTIONf_chiral_restr0.0291808
X-RAY DIFFRACTIONf_plane_restr0.0032015
X-RAY DIFFRACTIONf_dihedral_angle_d13.734484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6977-2.72830.40471410.34122724286581
2.7283-2.76040.32611830.31073289347299
2.7604-2.7940.33211540.30593317347199
2.794-2.82940.35911860.2873349353599
2.8294-2.86660.32361690.28843339350899
2.8666-2.90580.39281660.3043257342399
2.9058-2.94730.34091790.29023332351199
2.9473-2.99120.32011710.26673334350599
2.9912-3.03790.31891780.25843286346499
3.0379-3.08770.28191940.25953327352199
3.0877-3.14090.33841810.2483269345099
3.1409-3.19790.2721490.25253303345298
3.1979-3.25930.33171640.262133063470100
3.2593-3.32580.31231900.24932953485100
3.3258-3.3980.28261550.23293410356599
3.398-3.47690.23961710.21713280345199
3.4769-3.56370.26361780.20163241341999
3.5637-3.65990.2171660.19033399356599
3.6599-3.76740.22411460.184733773523100
3.7674-3.88880.212020.17673241344399
3.8888-4.02740.16872020.162433353537100
4.0274-4.18820.15892080.15743220342899
4.1882-4.37830.18792320.153332783510100
4.3783-4.60830.14331860.139133333519100
4.6083-4.89580.14381940.134333073501100
4.8958-5.27190.16061930.144133113504100
5.2719-5.79880.17691650.167933553520100
5.7988-6.62970.22171720.17233299347199
6.6297-8.32190.16961620.157733383500100
8.3219-29.61410.15491640.14523301346598

+
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