[English] 日本語
Yorodumi
- PDB-4iyh: The crystal structure of a secreted protein EsxB (SeMet-labeled, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iyh
TitleThe crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne
ComponentsSecreted protein EsxBSecretion
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center For Structural Genomics / MCSG
Function / homology
Function and homology information


HP0062-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
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.881 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 (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,65718
Polymers44,6044
Non-polymers1,05314
Water2,900161
1
A: Secreted protein EsxB
B: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8549
Polymers22,3022
Non-polymers5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-89 kcal/mol
Surface area8750 Å2
MethodPISA
2
C: Secreted protein EsxB
D: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8039
Polymers22,3022
Non-polymers5017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-94 kcal/mol
Surface area8720 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-197 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.337, 77.337, 71.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Secreted protein EsxB / Secretion


Mass: 11151.069 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis / Plasmid: pMCSG26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS

-
Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Na2HPO4:Citric Acid, 2.0M Ammonium Sulfate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.52
ReflectionResolution: 1.88→49 Å / Num. all: 38708 / Num. obs: 38708 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1928 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.881→48.792 Å / σ(F): 1.96 / Phase error: 16.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 1939 5.01 %random
Rwork0.1411 ---
obs0.145 38682 99.97 %-
all-38682 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.881→48.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 60 161 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062616
X-RAY DIFFRACTIONf_angle_d0.8063500
X-RAY DIFFRACTIONf_dihedral_angle_d15.351993
X-RAY DIFFRACTIONf_chiral_restr0.057366
X-RAY DIFFRACTIONf_plane_restr0.003465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8812-1.92830.21931500.21462593X-RAY DIFFRACTION94
1.9283-1.98040.21300.19582661X-RAY DIFFRACTION95
1.9804-2.03870.18811470.17692584X-RAY DIFFRACTION95
2.0387-2.10450.16951500.16252627X-RAY DIFFRACTION95
2.1045-2.17970.15851380.15142593X-RAY DIFFRACTION95
2.1797-2.26690.15131210.14362666X-RAY DIFFRACTION96
2.2669-2.370.17761190.14082634X-RAY DIFFRACTION96
2.37-2.49490.13731380.13882646X-RAY DIFFRACTION95
2.4949-2.65120.15971160.14032621X-RAY DIFFRACTION96
2.6512-2.85570.16071340.14032643X-RAY DIFFRACTION95
2.8557-3.14280.15411540.13732590X-RAY DIFFRACTION94
3.1428-3.5970.181320.13722636X-RAY DIFFRACTION95
3.597-4.52940.13691440.11392617X-RAY DIFFRACTION95
4.5294-30.30940.18461650.14932598X-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)
10.8188-0.04250.6860.5102-0.72095.4765-0.0602-0.19910.113-0.0082-0.02030.00090.0678-0.24120.01010.1047-0.03320.00820.1194-0.01690.1196-9.6243-1.61824.2804
21.498-0.0242-0.82841.65120.43288.1347-0.0704-0.1289-0.0498-0.1026-0.0348-0.05230.09180.17970.04950.0377-0.0290.00640.09980.00090.1658-11.2242-12.4210.9973
30.8040.106-0.37811.0093-1.15175.7824-0.0225-0.0487-0.0606-0.13580.01110.00040.0464-0.1079-0.02870.0741-0.0221-0.0040.1045-0.01070.1075-5.2416-7.335-5.0377
41.58360.1398-0.61821.40530.87656.1217-0.1330.01040.0727-0.12590.17640.0197-0.1521-0.0125-0.05570.0781-0.0267-0.00050.08230.02250.1412-15.7961-4.7164-6.1811
50.4058-0.0929-0.37421.10942.14089.4855-0.0542-0.0416-0.0137-0.0692-0.02750.0924-0.0899-0.10460.09920.0536-0.017-0.0010.11370.00450.122-33.4485-14.5999-0.5086
61.26880.20120.53880.85090.21173.4772-0.14390.070.0117-0.16980.0942-0.00620.1658-0.03960.01310.0966-0.04320.00010.09690.00430.1401-23.5794-18.802-6.2787
70.9398-0.1212-1.32960.70170.55144.9595-0.0768-0.1253-0.04570.00790.0591-0.0537-0.08540.2095-0.02190.0795-0.0237-0.00680.10040.00290.1248-29.7125-21.45043.9191
81.01850.2939-0.22131.4436-0.18813.05710.0363-0.29080.0619-0.0748-0.09320.0289-0.0437-0.12890.00190.0504-0.02310.02150.1728-0.00920.1215-26.5186-11.08315.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 84 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 47 )
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 84 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 42 )
6X-RAY DIFFRACTION6chain 'C' and (resid 43 through 85 )
7X-RAY DIFFRACTION7chain 'D' and (resid 5 through 47 )
8X-RAY DIFFRACTION8chain 'D' and (resid 48 through 84 )

+
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