[English] 日本語
Yorodumi
- PDB-4xy3: Structure of ESX-1 secreted protein EspB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xy3
TitleStructure of ESX-1 secreted protein EspB
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 Å
AuthorsWagner, J.M. / 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
DepositionFeb 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Structure summary
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Aug 5, 2015Group: Database references
Revision 1.4Sep 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 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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


Theoretical massNumber of molelcules
Total (without water)47,8331
Polymers47,8331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.110, 146.490, 94.220
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: 47832.730 Da / Num. of mol.: 1
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.8
Details: 0.1M CAPSO, PH 10.8, 0.2M sodium chloride, 1.5M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→47.11 Å / Num. all: 9916 / Num. obs: 9487 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.05 % / Biso Wilson estimate: 62.971 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.151 / Χ2: 0.933 / Net I/σ(I): 8.99 / Num. measured all: 47924
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.04-3.25.050.6350.9171.7334927036861.1797.5
3.12-3.20.8620.7772.0234886976790.85997.4
3.2-3.30.8490.5422.7833776896700.60297.2
3.3-3.40.9030.4323.432186586400.47997.3
3.4-3.510.9520.3284.3832006486260.36496.6
3.51-3.630.9780.2316.0331146286090.25697
3.63-3.770.9780.1817.4629906055830.20196.4
3.77-3.920.9760.1698.5928675835600.18896.1
3.92-4.10.9790.159.5327635725480.16795.8
4.1-4.30.9890.11911.0325675315080.13395.7
4.3-4.530.990.10412.4324815104900.11696.1
4.53-4.810.990.10113.1123764894690.11395.9
4.81-5.140.9940.09313.7722184574340.10395
5.14-5.550.990.113.2720444274030.11194.4
5.55-6.080.990.0914.1318393923670.10193.6
6.08-6.80.9950.07216.1317153673440.0893.7
6.8-7.850.9950.06318.3814933202990.0793.4
7.85-9.610.9980.05221.812432802560.05891.4
9.61-13.60.9980.04723.959592262020.05289.4
13.60.9960.05619.984801341140.06285.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XXN

4xxn


Resolution: 3.04→47.11 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2476 / WRfactor Rwork: 0.1966 / FOM work R set: 0.7093 / SU B: 23.513 / SU ML: 0.367 / SU R Cruickshank DPI: 0.8089 / SU Rfree: 0.3842 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.809 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 491 5.2 %RANDOM
Rwork0.2199 8999 --
obs0.2223 8999 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.75 Å2 / Biso mean: 82.474 Å2 / Biso min: 52.25 Å2
Baniso -1Baniso -2Baniso -3
1--4.12 Å20 Å20 Å2
2--9.75 Å20 Å2
3----5.63 Å2
Refinement stepCycle: final / Resolution: 3.04→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 0 0 1903
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191942
X-RAY DIFFRACTIONr_bond_other_d0.0010.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9562641
X-RAY DIFFRACTIONr_angle_other_deg0.89434207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57724.84899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79315319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2721515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_mcbond_it3.6857.939970
X-RAY DIFFRACTIONr_mcbond_other3.667.939969
X-RAY DIFFRACTIONr_mcangle_it6.10311.8971209
LS refinement shellResolution: 3.04→3.119 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 33 -
Rwork0.463 649 -
all-682 -
obs--97.15 %

+
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://pdbjlvh1.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