[English] 日本語
Yorodumi
- PDB-4j7k: The crystal structure of a secreted protein EsxB (Mutant E54Q) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j7k
TitleThe crystal structure of a secreted protein EsxB (Mutant E54Q) from Bacillus anthracis str. Sterne
Componentssecreted protein EsxB
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: 1.66 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 E54Q) 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 / 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: secreted protein EsxB
B: secreted protein EsxB
C: secreted protein EsxB
D: secreted protein EsxB


Theoretical massNumber of molelcules
Total (without water)41,4864
Polymers41,4864
Non-polymers00
Water6,413356
1
A: secreted protein EsxB
B: secreted protein EsxB


Theoretical massNumber of molelcules
Total (without water)20,7432
Polymers20,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-27 kcal/mol
Surface area10290 Å2
MethodPISA
2
C: secreted protein EsxB
D: secreted protein EsxB


Theoretical massNumber of molelcules
Total (without water)20,7432
Polymers20,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.274, 132.473, 38.347
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
secreted protein EsxB


Mass: 10371.541 Da / Num. of mol.: 4 / Mutation: E54Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17M Ammonium Acetate, 0.085M Sodium Acetate:HCl, 25.5%(w/v)PEG4000, 15%(v/v)Glycerol, pH 4.6, 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: 1.66→38 Å / Num. all: 35247 / Num. obs: 35247 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 27
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1500 / % possible all: 83

-
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: 1.66→38 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1758 5 %random
Rwork0.1752 ---
obs0.1774 35187 96.76 %-
all-35187 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 356 3162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052854
X-RAY DIFFRACTIONf_angle_d0.9333830
X-RAY DIFFRACTIONf_dihedral_angle_d16.6531096
X-RAY DIFFRACTIONf_chiral_restr0.067408
X-RAY DIFFRACTIONf_plane_restr0.005519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6602-1.70510.27441180.22932186X-RAY DIFFRACTION83
1.7051-1.75530.25241230.21542379X-RAY DIFFRACTION89
1.7553-1.81190.24491240.21412548X-RAY DIFFRACTION96
1.8119-1.87670.25491460.20482589X-RAY DIFFRACTION99
1.8767-1.95180.27251640.19782673X-RAY DIFFRACTION100
1.9518-2.04060.22421170.19522637X-RAY DIFFRACTION100
2.0406-2.14820.22081300.1712658X-RAY DIFFRACTION100
2.1482-2.28280.20311270.16442678X-RAY DIFFRACTION100
2.2828-2.4590.20391390.16882656X-RAY DIFFRACTION100
2.459-2.70640.21821140.16352679X-RAY DIFFRACTION100
2.7064-3.09790.22791570.17372643X-RAY DIFFRACTION100
3.0979-3.90240.18011590.15442567X-RAY DIFFRACTION97
3.9024-38.01780.21621400.17562536X-RAY DIFFRACTION95
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)
11.8456-1.35710.21882.82081.40478.82170.0925-0.44790.08050.66870.10090.7523-0.0609-0.7835-0.28750.31060.01610.07690.31240.00640.27550.241428.64113.1764
2-0.010.86270.22066.63320.2435-0.02410.0095-0.0026-0.06540.06520.0108-0.360.00910.0389-0.00590.182-0.00740.0070.1768-0.00180.197.86611.40660.5204
30.36671.04690.16786.44110.340.0515-0.05820.0081-0.0028-0.56210.0687-0.0865-0.04470.00780.01750.2568-0.00830.00530.20190.00160.14414.49168.2857-5.6657
40.1402-0.04290.12072.4863-0.56670.4255-0.0112-0.0006-0.07480.04080.08420.29150.0017-0.0239-0.07340.1268-0.0040.00360.1774-0.00410.16820.4429-3.21415.2111
50.37460.0943-0.05475.2646-0.89780.52690.0012-0.0101-0.02520.01080.00890.4498-0.0113-0.018-0.06640.1235-0.0021-0.0360.1652-0.00570.1697-4.591-4.57850.8193
60.40080.31960.10381.18250.06621.3203-0.0025-0.0257-0.01970.15340.02260.00840.1711-0.0738-0.00360.0939-0.01260.0110.17630.00520.118510.004526.1937-16.5792
70.68660.49610.37434.71930.63420.9623-0.02440.0481-0.065-0.27580.1032-0.06790.20950.0615-0.07220.1785-0.00120.02380.1976-0.00670.111313.999722.6584-24.11
81.3092-0.62260.35485.67950.47161.1474-0.0655-0.05910.113-0.03380.0794-0.0168-0.00760.0018-0.01720.0817-0.00690.01420.1945-0.00340.113314.822137.2474-12.3519
91.4463-0.21160.50015.40330.82511.46-0.00170.0775-0.05980.19880.1651-0.51960.18850.1305-0.19540.10940.01660.01130.22420.00030.149622.124731.7295-16.3316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 88 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 90 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 44 )
7X-RAY DIFFRACTION7chain 'C' and (resid 45 through 90 )
8X-RAY DIFFRACTION8chain 'D' and (resid 3 through 39 )
9X-RAY DIFFRACTION9chain 'D' and (resid 40 through 86 )

+
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