[English] 日本語
Yorodumi
- PDB-6swz: Structure of the C-terminal domain of C. glutamicum mycoloyltrans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6swz
TitleStructure of the C-terminal domain of C. glutamicum mycoloyltransferase A
ComponentsProtein PS1
KeywordsTRANSFERASE / Mycoloyltransferase / Mycolic acid / cell wall
Function / homologyLGFP / LGFP repeat / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold / extracellular region / Protein PS1
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsLi de la Sierra-Gallay, I. / Van tilbeurgh, H. / Bayan, N.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
CitationJournal: Mol.Microbiol. / Year: 2020
Title: The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability.
Authors: Dietrich, C. / Li de la Sierra-Gallay, I. / Masi, M. / Girard, E. / Dautin, N. / Constantinesco-Becker, F. / Tropis, M. / Daffe, M. / van Tilbeurgh, H. / Bayan, N.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4133
Polymers28,2291
Non-polymers1842
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-2 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 57.670, 83.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein PS1


Mass: 28228.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: csp1, cop1, Cgl2875, cg3182 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P0C1D6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.04 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.2 to 1.4 M NaCl, 0.1M Na Acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 9, 2016
RadiationMonochromator: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.995→41.735 Å / Num. obs: 16219 / % possible obs: 99.4 % / Redundancy: 7.26 % / CC1/2: 0.99 / Rrim(I) all: 0.115 / Net I/σ(I): 11.46
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 1.54 / Num. unique obs: 2484 / CC1/2: 0.64 / Rrim(I) all: 1.25

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→41.735 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.184 / Average fsc free: 0.8323 / Average fsc work: 0.8651 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2584 811 5 %
Rwork0.1981 15408 -
all0.201 --
obs-16219 99.363 %
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: 36.766 Å2
Baniso -1Baniso -2Baniso -3
1--2.471 Å20 Å20 Å2
2--3.106 Å20 Å2
3----0.635 Å2
Refinement stepCycle: LAST / Resolution: 1.995→41.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 12 77 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121752
X-RAY DIFFRACTIONr_bond_other_d0.0370.0181491
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6422375
X-RAY DIFFRACTIONr_angle_other_deg2.4041.5743460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6345219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20722.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3821510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022055
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02419
X-RAY DIFFRACTIONr_nbd_refined0.1840.2342
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.21465
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2858
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.210
X-RAY DIFFRACTIONr_nbd_other0.2240.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.26
X-RAY DIFFRACTIONr_mcbond_it2.7433.862873
X-RAY DIFFRACTIONr_mcbond_other2.7333.858872
X-RAY DIFFRACTIONr_mcangle_it3.9585.781093
X-RAY DIFFRACTIONr_mcangle_other3.9575.7851094
X-RAY DIFFRACTIONr_scbond_it3.1314.025879
X-RAY DIFFRACTIONr_scbond_other3.1294.025880
X-RAY DIFFRACTIONr_scangle_it4.5285.9411282
X-RAY DIFFRACTIONr_scangle_other4.5265.9421283
X-RAY DIFFRACTIONr_lrange_it6.45443.7562014
X-RAY DIFFRACTIONr_lrange_other6.4443.7092010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.0470.497530.4011017X-RAY DIFFRACTION92.0034
2.047-2.1030.421580.3611094X-RAY DIFFRACTION99.9133

+
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