[English] 日本語
Yorodumi
- PDB-6h35: Myxococcus xanthus MglA bound to GDP and Pi with mixed inactive a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h35
TitleMyxococcus xanthus MglA bound to GDP and Pi with mixed inactive and active switch region conformations
ComponentsMutual gliding-motility protein MglA
KeywordsCYTOSOLIC PROTEIN / small GTPase in a mixed state
Function / homology
Function and homology information


regulation of protein localization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
: / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVarela, P.F. / Galicia, C. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: Nat Commun / Year: 2019
Title: MglA functions as a three-state GTPase to control movement reversals of Myxococcus xanthus.
Authors: Galicia, C. / Lhospice, S. / Varela, P.F. / Trapani, S. / Zhang, W. / Navaza, J. / Herrou, J. / Mignot, T. / Cherfils, J.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mutual gliding-motility protein MglA
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78714
Polymers45,7432
Non-polymers2,04512
Water2,792155
1
A: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1189
Polymers22,8711
Non-polymers1,2478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6695
Polymers22,8711
Non-polymers7984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.600, 116.650, 49.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-455-

HOH

-
Components

#1: Protein Mutual gliding-motility protein MglA


Mass: 22871.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Small GTPase / Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 93193 / % possible obs: 74.71 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.076 / Net I/σ(I): 8.29
Reflection shellResolution: 2.299→2.38 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 474 / CC1/2: 0.392 / % possible all: 20.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.11 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9156 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 848 4.85 %random
Rwork0.2135 16624 --
obs0.2155 17472 74.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 133 155 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343272
X-RAY DIFFRACTIONf_angle_d0.76374441
X-RAY DIFFRACTIONf_chiral_restr0.0475500
X-RAY DIFFRACTIONf_plane_restr0.0042544
X-RAY DIFFRACTIONf_dihedral_angle_d7.84892319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.3584490.3362804X-RAY DIFFRACTION22.25
2.44-2.630.3177690.29631392X-RAY DIFFRACTION38.26
2.63-2.90.29181570.28243157X-RAY DIFFRACTION86.06
2.9-3.320.27621850.22523676X-RAY DIFFRACTION99.87
3.32-4.180.23281960.18493719X-RAY DIFFRACTION99.92
4.18-49.120.24531920.1993876X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: 32.303813486 Å / Origin y: 14.7277344099 Å / Origin z: 70.125826273 Å
111213212223313233
T0.151727455952 Å20.0318632340516 Å20.000714965373303 Å2-0.157843902047 Å20.00456517040674 Å2--0.133104574667 Å2
L0.825014828201 °20.166458797225 °2-0.115500401313 °2-1.2346168088 °2-0.385856557353 °2--0.457698060692 °2
S-0.0460762224911 Å °0.0402299587653 Å °-0.0186976574689 Å °0.0617549787103 Å °0.10560452117 Å °0.143531617216 Å °0.0145643759255 Å °0.018149100068 Å °0.00895288325152 Å °
Refinement TLS groupSelection details: all

+
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