[English] 日本語
Yorodumi
- PDB-4j7j: The crystal structure of a secreted protein EsxB (Mutant G53A) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j7j
TitleThe crystal structure of a secreted protein EsxB (Mutant G53A) from Bacillus anthracis str. Sterne
Componentssecreted protein EsxBSecretion
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHP0062-like domain superfamily / HP0062-like domain / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / ESAT-6-like protein / ESAT-6-like protein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.458 Å
AuthorsFan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a secreted protein EsxB (Mutant, G53A) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: secreted protein EsxB
B: secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8653
Polymers20,7732
Non-polymers921
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.064, 38.445, 130.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein secreted protein EsxB / Secretion


Mass: 10386.552 Da / Num. of mol.: 2 / Mutation: G53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis, BAS2036, BA_2191, GBAA_2191 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium Acetate:HCl, 25% (w/v) PEG3350 , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. all: 29127 / Num. obs: 29127 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 36.1
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 4 / Num. unique all: 1222 / % possible all: 82.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J11

4j11


Resolution: 1.458→29.494 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1471 5.07 %Random
Rwork0.1824 ---
obs0.1841 29023 96.79 %-
all-29023 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.458→29.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 6 199 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061410
X-RAY DIFFRACTIONf_angle_d0.9821892
X-RAY DIFFRACTIONf_dihedral_angle_d15.756549
X-RAY DIFFRACTIONf_chiral_restr0.065203
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4576-1.50460.27851130.23252142X-RAY DIFFRACTION84
1.5046-1.55840.26091260.20382375X-RAY DIFFRACTION94
1.5584-1.62080.26911340.17782526X-RAY DIFFRACTION99
1.6208-1.69460.21881420.17152528X-RAY DIFFRACTION100
1.6946-1.78390.19641280.17662548X-RAY DIFFRACTION100
1.7839-1.89560.23231140.17372578X-RAY DIFFRACTION100
1.8956-2.0420.23971300.18832584X-RAY DIFFRACTION99
2.042-2.24740.24291210.17592561X-RAY DIFFRACTION99
2.2474-2.57240.20791670.17822531X-RAY DIFFRACTION99
2.5724-3.24040.22041600.18632572X-RAY DIFFRACTION98
3.2404-29.49970.1881360.18082607X-RAY DIFFRACTION94
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)
10.6661-0.1135-0.01491.3626-0.26894.4059-0.05350.06380.0289-0.0257-0.00990.01330.1708-0.15690.0660.0756-0.00320.00420.07920.00690.1413-1.24342.358722.2775
20.7482-0.0606-0.29651.60110.38947.73910.05170.0224-0.043-0.1289-0.0701-0.11870.469-0.04320.0110.15290.01030.00430.07270.00480.14792.734-5.104523.5118
31.998-0.3581-0.8740.30820.62481.27380.04610.7894-0.6439-0.1835-0.23480.06280.5407-0.31560.17830.4907-0.0273-0.03650.5131-0.0920.2634-3.51980.139-13.2539
41.3594-0.19861.3220.7823-0.82398.6229-0.07090.03810.12670.082-0.0826-0.1211-0.22850.19380.18780.1028-0.0064-0.01570.11680.0080.16615.00827.16919.4048
51.8492-0.30731.45561.0414-0.98257.6121-0.0190.25060.0693-0.0642-0.1692-0.18590.23460.76460.21250.0820.0280.00160.17910.01690.17469.66091.694513.8202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 90 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 85 )

+
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