[English] 日本語
Yorodumi
- PDB-7ct3: Crystal Structure of MglC from Myxococcus xanthus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ct3
TitleCrystal Structure of MglC from Myxococcus xanthus
ComponentsMutual gliding motility protein C (MglC)
KeywordsCYTOSOLIC PROTEIN / Roadblock/LC7 domain
Function / homologyPredicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsThakur, K.G. / Kapoor, S. / Kodesia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB.
Authors: Kapoor, S. / Kodesia, A. / Kalidas, N. / Thakur, K.G.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 2.0Apr 28, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / refine / refine_hist / software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.details / _refine_hist.pdbx_B_iso_mean_ligand / _software.classification / _software.name / _software.version
Description: Ligand identity / Details: Mg2+ is replaced with Na+ / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mutual gliding motility protein C (MglC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2992
Polymers13,2761
Non-polymers231
Water1,24369
1
A: Mutual gliding motility protein C (MglC)
hetero molecules

A: Mutual gliding motility protein C (MglC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5974
Polymers26,5512
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area1860 Å2
ΔGint-31 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.690, 96.690, 58.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

-
Components

#1: Protein Mutual gliding motility protein C (MglC)


Mass: 13275.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Strain: DK 1622 / Gene: MXAN_5770 / Plasmid: pET-Duet-A-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D0B6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium Sulfate Monohydrate, 0.1 M Tris-HCl pH 8.5, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2020 / Details: LN2 closed loop cooling
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→29.14 Å / Num. obs: 14178 / % possible obs: 99.9 % / Redundancy: 16 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.022 / Rrim(I) all: 0.089 / Net I/σ(I): 21.3 / Num. measured all: 226964 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.8916.91.455142528450.7570.361.52.699.6
9.06-29.1410.80.033168715610.010.03549.695.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
AutoSol1.12phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→27.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.198 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 713 5 %RANDOM
Rwork0.1578 ---
obs0.1604 13444 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.68 Å2 / Biso mean: 36.605 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å2-0 Å2
2--1.08 Å20 Å2
3----3.49 Å2
Refinement stepCycle: final / Resolution: 1.85→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 1 69 991
Biso mean--30 53.19 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.013934
X-RAY DIFFRACTIONr_bond_other_d0.0010.017884
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.6361266
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5722039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9665119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57122.55347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58715151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.582156
X-RAY DIFFRACTIONr_chiral_restr0.0540.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_rigid_bond_restr0.93531817
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 61 -
Rwork0.237 947 -
all-1008 -
obs--99.51 %

+
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