[English] 日本語
Yorodumi
- PDB-4rcl: Structure of EspG3 chaperone from the type VII (ESX-3) secretion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rcl
TitleStructure of EspG3 chaperone from the type VII (ESX-3) secretion system, space group P43212
ComponentsESPG3
KeywordsCHAPERONE / ESX-3 / type VII secretion system / RV0289 / protein secretion
Function / homologyEspG family / EspG family / cytoplasm / ESX-3 secretion-associated protein EspG3
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKorotkov, K.V.
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems.
Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / ...Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / Parret, A.H.A. / Korotkov, K.V.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / 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 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESPG3
B: ESPG3


Theoretical massNumber of molelcules
Total (without water)63,7342
Polymers63,7342
Non-polymers00
Water25214
1
A: ESPG3


Theoretical massNumber of molelcules
Total (without water)31,8671
Polymers31,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ESPG3


Theoretical massNumber of molelcules
Total (without water)31,8671
Polymers31,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.679, 92.679, 158.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ESPG3


Mass: 31866.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0622, MSMEI_0606 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0QQ45
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 295 K / pH: 6
Details: 0.1M SODIUM CACODYLATE, PH 6.0, 15% PEG200, 5% PEG3350, vapor diffusion, hanging drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→46.34 Å / Num. obs: 36408 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 67.77 Å2 / Rsym value: 0.087 / Net I/σ(I): 19.8
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 138.9 / % possible all: 99.3

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L4W

4l4w


Resolution: 2.7→46.34 Å / SU ML: 0.44 / σ(F): 1.16 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1852 5.09 %
Rwork0.23 --
obs0.233 36397 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 0 14 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033798
X-RAY DIFFRACTIONf_angle_d0.7225195
X-RAY DIFFRACTIONf_dihedral_angle_d10.5321340
X-RAY DIFFRACTIONf_chiral_restr0.03601
X-RAY DIFFRACTIONf_plane_restr0.004679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76930.4011440.34772621X-RAY DIFFRACTION98
2.7693-2.85080.3841230.32352690X-RAY DIFFRACTION100
2.8508-2.94280.36351390.32742646X-RAY DIFFRACTION100
2.9428-3.04790.33441510.29062662X-RAY DIFFRACTION100
3.0479-3.170.38131430.29912656X-RAY DIFFRACTION100
3.17-3.31420.3171730.26742618X-RAY DIFFRACTION100
3.3142-3.48890.2631570.25172668X-RAY DIFFRACTION100
3.4889-3.70740.25131600.24852660X-RAY DIFFRACTION100
3.7074-3.99350.31521490.23022628X-RAY DIFFRACTION100
3.9935-4.39510.24521480.21282671X-RAY DIFFRACTION100
4.3951-5.03040.20081090.17232673X-RAY DIFFRACTION100
5.0304-6.33520.28281550.21212654X-RAY DIFFRACTION100
6.3352-46.34630.23781010.20532698X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.76680.62921.63644.58040.21132.4392-0.2666-0.11420.53890.4740.1501-0.5696-0.56080.58030.20010.8273-0.3355-0.06010.9183-0.13230.85457.47329.407-15.092
23.3443.2586-0.75226.1599-1.18542.88660.1506-0.08340.09820.0028-0.0247-0.3004-0.44620.7298-0.11390.4785-0.10170.0480.4054-0.05230.3968-3.07313.143-19.58
37.99622.07034.05033.6137-1.07138.4616-0.0544-0.7998-0.21550.7802-0.03130.1186-0.5049-0.3137-0.08350.7630.1621-0.04010.63940.04190.6264-16.905-2.053-0.7
42.6095-0.9209-0.3893.5681-0.27223.04120.0087-0.23720.1763-0.1125-0.0366-0.0895-0.22910.20160.01980.4559-0.00080.03010.2383-0.02170.3969-14.2425.64-16.825
52.8176-0.5890.45043.5339-0.07970.8972-0.0789-0.7676-0.77480.9843-0.0783-0.19980.83770.12790.08421.99820.22810.13260.5560.22720.7616-23.30521.3743.604
62.35241.6152-1.91044.8487-2.70154.6295-0.0986-0.3406-0.17091.65490.04240.0038-0.17220.14030.09661.13070.12790.0060.4480.00120.5406-25.32936.333-1.95
75.98240.9203-2.13482.90071.82942.50450.70550.1020.65890.7410.005-1.04820.76582.2066-0.91320.86180.0691-0.25811.452-0.31291.1214-6.63348.391-9.599
83.36-0.4759-0.1294.7224-0.6022.1423-0.2-0.1855-0.23931.05560.0082-0.02030.41020.07360.07730.84580.0229-0.00180.2833-0.00510.5202-23.41636.329-11.937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:64 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 65:151 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 152:180 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 181:265 )
5X-RAY DIFFRACTION5(CHAIN B AND RESID 2:100 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 101:156 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 157:191 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 192:265 )

+
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