[English] 日本語
Yorodumi
- PDB-6c9o: Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c9o
TitleSelenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Immunoglobulin G-binding protein G protein
Function / homology
Function and homology information


Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsChen, Q.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1616178 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 P30 GM110758-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 P20 GM104316 United States
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: 77Se NMR Probes the Protein Environment of Selenomethionine.
Authors: Chen, Q. / Xu, S. / Lu, X. / Boeri, M.V. / Pepelyayeva, Y. / Diaz, E.L. / Soni, S.D. / Allaire, M. / Forstner, M.B. / Bahnson, B.J. / Rozovsky, S.
History
DepositionJan 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 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
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9406
Polymers12,4672
Non-polymers4734
Water3,009167
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4703
Polymers6,2341
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4703
Polymers6,2341
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.506, 36.497, 48.843
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6233.625 Da / Num. of mol.: 2 / Mutation: V29M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Cell line (production host): BL21DE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 46% MPD, 20% IPA, 25 mM sodium acetate pH 4.5 / PH range: 4.5-4.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2017
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→29.1 Å / Num. obs: 29169 / % possible obs: 97.03 % / Redundancy: 2 % / Biso Wilson estimate: 9.47 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.02561 / Rpim(I) all: 0.02561 / Rrim(I) all: 0.03622 / Net I/σ(I): 9.36
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1201 / Num. unique obs: 2768 / CC1/2: 0.979 / Rpim(I) all: 0.1201 / Rrim(I) all: 0.1698 / % possible all: 93.82

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 1.2→29.099 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2491 4.41 %1283
Rwork0.151 ---
obs0.1522 56546 96.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→29.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 40 167 1077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01928
X-RAY DIFFRACTIONf_angle_d1.3381263
X-RAY DIFFRACTIONf_dihedral_angle_d19.612324
X-RAY DIFFRACTIONf_chiral_restr0.251145
X-RAY DIFFRACTIONf_plane_restr0.006156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22310.18761310.1772860X-RAY DIFFRACTION92
1.2231-1.24810.26111340.17132889X-RAY DIFFRACTION93
1.2481-1.27520.22821330.16932893X-RAY DIFFRACTION93
1.2752-1.30490.1961310.15552953X-RAY DIFFRACTION94
1.3049-1.33750.19851340.15222911X-RAY DIFFRACTION95
1.3375-1.37360.18311420.153023X-RAY DIFFRACTION96
1.3736-1.41410.17611350.14542967X-RAY DIFFRACTION96
1.4141-1.45970.20121360.14282994X-RAY DIFFRACTION96
1.4597-1.51190.16721430.13123025X-RAY DIFFRACTION97
1.5119-1.57240.16531410.13043023X-RAY DIFFRACTION97
1.5724-1.6440.1761370.12813022X-RAY DIFFRACTION97
1.644-1.73060.16931400.14163050X-RAY DIFFRACTION98
1.7306-1.8390.19571410.14913046X-RAY DIFFRACTION98
1.839-1.9810.17381430.13173074X-RAY DIFFRACTION99
1.981-2.18030.17341410.13253062X-RAY DIFFRACTION98
2.1803-2.49560.17351460.15113090X-RAY DIFFRACTION99
2.4956-3.14370.17451420.15823091X-RAY DIFFRACTION99
3.1437-29.10740.17021410.17173082X-RAY DIFFRACTION99

+
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