[English] 日本語
Yorodumi
- PDB-4xxx: Structure of PE-PPE domains of ESX-1 secreted protein EspB, C2221 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xxx
TitleStructure of PE-PPE domains of ESX-1 secreted protein EspB, C2221
ComponentsESX-1 secretion-associated protein EspB
KeywordsPROTEIN TRANSPORT / ESX-1 / type VII secretion system / secreted protein / PE domain / PPE domain
Function / homologyESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / protein secretion by the type VII secretion system / PPE superfamily / biological process involved in interaction with host / extracellular region / identical protein binding / ESX-1 secretion-associated protein EspB
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsPiton, J. / Pojer, F. / Korotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis.
Authors: Korotkova, N. / Piton, J. / Wagner, J.M. / Boy-Rottger, S. / Japaridze, A. / Evans, T.J. / Cole, S.T. / Pojer, F. / Korotkov, K.V.
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESX-1 secretion-associated protein EspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2094
Polymers29,9891
Non-polymers2203
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.336, 69.579, 119.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein ESX-1 secretion-associated protein EspB / Antigen MTB48


Mass: 29989.094 Da / Num. of mol.: 1 / Fragment: UNP residues 7-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: espB, mtb48, Rv3881c, MTV027.16c / Plasmid: pRSF-NT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P9WJD9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 0.2 M potassium dihydrogen phosphate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2014
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→59.797 Å / Num. all: 44932 / Num. obs: 44932 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.6 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.052 / Rsym value: 0.047 / Net I/av σ(I): 12.675 / Net I/σ(I): 18.6 / Num. measured all: 241572
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.585.10.74723263863690.3650.747298.3
1.58-1.685.30.5311.53280761810.2550.5312.999.9
1.68-1.85.20.3672.13000958090.1790.3674.299.9
1.8-1.945.70.223.53100454090.1010.227.1100
1.94-2.125.70.1266.22820249800.0580.12612.3100
2.12-2.385.30.07112383445260.0340.0720.399.9
2.38-2.745.50.04317.32194940140.020.04331.699.9
2.74-3.365.60.02824.51928634280.0130.02848.499.9
3.36-4.755.10.01931.51343026590.0090.0196999.2
4.75-44.8555.40.01634841315570.0070.01671.199.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
SCALA3.3.22data scaling
REFMAC5.8.0103phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4XWP

4xwp


Resolution: 1.5→59.797 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1927 / WRfactor Rwork: 0.1699 / FOM work R set: 0.7773 / SU B: 4.022 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0765 / SU Rfree: 0.0765 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2191 4.9 %RANDOM
Rwork0.1937 42701 --
obs0.1949 42701 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.83 Å2 / Biso mean: 27.775 Å2 / Biso min: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--1.24 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.5→59.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 13 263 2220
Biso mean--35.98 36.58 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192022
X-RAY DIFFRACTIONr_bond_other_d0.0020.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9562749
X-RAY DIFFRACTIONr_angle_other_deg0.94234350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0595253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96325106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88815331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.951516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_mcbond_it0.8531.5071009
X-RAY DIFFRACTIONr_mcbond_other0.851.5061008
X-RAY DIFFRACTIONr_mcangle_it1.362.2511263
LS refinement shellResolution: 1.5→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 165 -
Rwork0.404 3010 -
all-3175 -
obs--96.48 %
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)
10.17820.1430.04054.11071.38110.7170.0186-0.0127-0.0092-0.00550.00010.0622-0.11870.003-0.01870.18480.0213-0.02310.0122-0.00980.021719.81540.48242.233
20.01360.25790.348613.874810.759311.1466-0.0147-0.02260.01370.0177-0.50910.8481-0.3642-0.52860.52390.21520.02890.01420.0795-0.07090.107314.46362.20251.735
30.51.6330.606119.31895.20071.6398-0.1124-0.13780.12480.4521-0.151.1771-0.0336-0.04340.26240.23220.00560.0460.0644-0.03920.100410.73744.648.977
41.59340.1709-0.45156.02231.14212.2494-0.0328-0.0105-0.19920.3753-0.01580.25690.139-0.19130.04860.11790.0234-0.03270.0303-0.01480.089621.8928.16731.513
50.29620.1443-0.12885.72122.22651.58380.0795-0.0002-0.01630.52540.0783-0.29820.0720.1258-0.15780.23190.0144-0.07120.0189-0.01830.03525.45443.15550.127
60.6145-0.0760.14065.30451.20961.0552-0.07980.0212-0.065-0.00730.0441-0.1335-0.0117-0.00190.03570.09870.0067-0.01660.0548-0.01510.111929.363-1.3130.429
71.3544-3.472-1.081812.10982.81610.8875-0.2082-0.0931-0.07320.35470.14480.15340.10480.06660.06340.20420.0272-0.01630.0428-0.00220.044822.6647.5341.012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 68
2X-RAY DIFFRACTION2A69 - 83
3X-RAY DIFFRACTION3A84 - 124
4X-RAY DIFFRACTION4A125 - 150
5X-RAY DIFFRACTION5A151 - 209
6X-RAY DIFFRACTION6A210 - 245
7X-RAY DIFFRACTION7A246 - 278

+
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