[English] 日本語
Yorodumi
- PDB-6xpl: CutR Screw, form 2 with 33.8 angstrom pitch -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xpl
TitleCutR Screw, form 2 with 33.8 angstrom pitch
ComponentsEthanolamine utilization protein EutS
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / BMC
Function / homologyBacterial microcompartment shell protein EutS/PduU/CutR / bacterial microcompartment / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Bacterial microcompartment shell protein CutR
Function and homology information
Biological speciesStreptococcus intermedius SK54 = ATCC 27335 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsOchoa, J.M. / Sawaya, M.R. / Nguyen, V.N. / Duilio, C. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci. / Year: 2020
Title: Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.
Authors: Ochoa, J.M. / Nguyen, V.N. / Nie, M. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
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.identifier_ORCID / _citation_author.name
Revision 1.2Nov 11, 2020Group: 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.identifier_ORCID
Revision 1.3Jun 30, 2021Group: Data collection / Category: pdbx_reflns_twin
Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.4Oct 18, 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: Ethanolamine utilization protein EutS


Theoretical massNumber of molelcules
Total (without water)13,2801
Polymers13,2801
Non-polymers00
Water0
1
A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS


Theoretical massNumber of molelcules
Total (without water)79,6806
Polymers79,6806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+5/61
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)64.910, 64.910, 33.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Ethanolamine utilization protein EutS


Mass: 13280.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius SK54 = ATCC 27335 (bacteria)
Gene: HMPREF1654_00416 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2IV13

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.55 Å3/Da / Density % sol: 20.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris propane, 8.52% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7363
pseudo-merohedral11-K, -H, -L20.2637
ReflectionResolution: 3.3→56.214 Å / Num. obs: 1286 / % possible obs: 99.3 % / Redundancy: 4.579 % / Biso Wilson estimate: 81.695 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.236 / Rrim(I) all: 0.268 / Χ2: 0.755 / Net I/σ(I): 4.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.54.5431.3370.982080.5111.5199.5
3.5-3.764.2290.9311.52050.4641.06799
3.76-3.975.0850.6362.231180.8750.709100
3.97-4.214.8780.5052.621230.880.565100
4.21-4.864.7650.3254.672210.9240.365100
4.86-5.954.7860.3024.731820.9530.34100
5.95-8.44.2070.168.151450.9790.18498.6
8.4-56.2144.0710.04721.23840.9960.05495.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å56.21 Å
Translation3.7 Å56.21 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XPK

6xpk


Resolution: 3.3→56.214 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.918 / SU B: 30.858 / SU ML: 0.464 / Cross valid method: FREE R-VALUE / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2654 151 11.797 %
Rwork0.2193 1129 -
all0.225 --
obs-1280 99.533 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 123.909 Å2
Baniso -1Baniso -2Baniso -3
1--50.17 Å2-0 Å2-0 Å2
2---50.17 Å2-0 Å2
3---100.34 Å2
Refinement stepCycle: LAST / Resolution: 3.3→56.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 0 0 720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013731
X-RAY DIFFRACTIONr_bond_other_d0.0010.017686
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0110.012762
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.623997
X-RAY DIFFRACTIONr_angle_other_deg1.0691.5651589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0125.35728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0315114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.338151
X-RAY DIFFRACTIONr_chiral_restr0.0370.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_nbd_refined0.1530.2123
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1590.2622
X-RAY DIFFRACTIONr_nbtor_refined0.1440.2351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.27
X-RAY DIFFRACTIONr_nbd_other0.1850.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.22
X-RAY DIFFRACTIONr_mcbond_it19.98212.853391
X-RAY DIFFRACTIONr_mcbond_other19.95512.851390
X-RAY DIFFRACTIONr_mcangle_it28.38619.01487
X-RAY DIFFRACTIONr_mcangle_other28.37719.009488
X-RAY DIFFRACTIONr_scbond_it19.9914.232340
X-RAY DIFFRACTIONr_scbond_other20.00614.234339
X-RAY DIFFRACTIONr_scangle_it29.57720.748510
X-RAY DIFFRACTIONr_scangle_other29.55920.739510
X-RAY DIFFRACTIONr_lrange_it39.99313.8332833
X-RAY DIFFRACTIONr_lrange_other40.001313.8232829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.3860.296130.33479X-RAY DIFFRACTION96.8421
3.386-3.4780.27570.33991X-RAY DIFFRACTION100
3.478-3.5790.335100.25966X-RAY DIFFRACTION97.4359
3.579-3.6880.34890.29979X-RAY DIFFRACTION100
3.688-3.8090.214160.25167X-RAY DIFFRACTION100
3.809-3.9420.271100.21764X-RAY DIFFRACTION100
3.942-4.090.21450.25484X-RAY DIFFRACTION100
4.09-4.2560.45880.25363X-RAY DIFFRACTION100
4.256-4.4440.207120.17558X-RAY DIFFRACTION100
4.444-4.6590.16950.16667X-RAY DIFFRACTION100
4.659-4.910.15570.14160X-RAY DIFFRACTION100
4.91-5.2050.31160.15456X-RAY DIFFRACTION100
5.205-5.5610.5780.24150X-RAY DIFFRACTION100
5.561-6.0010.38970.20549X-RAY DIFFRACTION100
6.001-6.5670.39760.25147X-RAY DIFFRACTION100
6.567-7.3290.23650.19542X-RAY DIFFRACTION97.9167
7.329-8.4390.3560.13834X-RAY DIFFRACTION100
8.439-10.2780.10750.12332X-RAY DIFFRACTION100
10.278-14.2990.15340.17124X-RAY DIFFRACTION100
14.299-56.2140.47620.42517X-RAY DIFFRACTION100

+
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