[English] 日本語
Yorodumi
- PDB-5cpc: Crystal structure of SopD, a type III secreted virulence effector... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cpc
TitleCrystal structure of SopD, a type III secreted virulence effector from Salmonella enterica
ComponentsSecreted effector protein SopD
KeywordsCELL INVASION / T3SS effector protein / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologySalmonella outer protein D / Salmonella outer protein D / protein secretion by the type III secretion system / host cell cytosol / host cell membrane / host cell plasma membrane / extracellular region / membrane / Secreted effector protein SopD
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsShi, R. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: Cell Rep / Year: 2015
Title: Salmonella Disrupts Host Endocytic Trafficking by SopD2-Mediated Inhibition of Rab7.
Authors: D'Costa, V.M. / Braun, V. / Landekic, M. / Shi, R. / Proteau, A. / McDonald, L. / Cygler, M. / Grinstein, S. / Brumell, J.H.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Secreted effector protein SopD
B: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)72,3762
Polymers72,3762
Non-polymers00
Water1,964109
1
A: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)36,1881
Polymers36,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)36,1881
Polymers36,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.525, 102.743, 76.018
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Secreted effector protein SopD / Salmonella outer protein D


Mass: 36188.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sopD, STM2945 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40722
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 0.1M HEPES pH 7, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37360 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.064 / Χ2: 2.245 / Net I/av σ(I): 54.3 / Net I/σ(I): 17.4 / Num. measured all: 280209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.237.60.52137611.218100
2.23-2.327.60.3937451.245100
2.32-2.427.70.25737581.249100
2.42-2.557.70.18337461.352100
2.55-2.717.70.12637781.475100
2.71-2.927.70.08637711.663100
2.92-3.217.70.07137562.358100
3.21-3.687.20.06537854.091100
3.68-4.636.90.05737664.8199.8
4.63-507.20.04534943.57290.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2555 / WRfactor Rwork: 0.2225 / FOM work R set: 0.8022 / SU B: 14.162 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2405 / SU Rfree: 0.1916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1867 5 %RANDOM
Rwork0.2122 ---
obs0.2138 35455 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 55.801 Å2 / Biso min: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0.64 Å2
2---0.66 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 0 109 4582
Biso mean---42.27 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224570
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9476170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99725.024211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84215841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1221516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213397
X-RAY DIFFRACTIONr_mcbond_it1.0661.52801
X-RAY DIFFRACTIONr_mcangle_it1.97524526
X-RAY DIFFRACTIONr_scbond_it3.23931769
X-RAY DIFFRACTIONr_scangle_it4.8954.51643
LS refinement shellResolution: 2.15→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 141 -
Rwork0.267 2540 -
all-2681 -
obs--96.89 %
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)
10.21910.0510.76420.03940.28134.0185-0.08970.0488-0.02530.00660.0514-0.02880.07360.07250.03820.1726-0.07490.01970.1461-0.05670.1153-0.3110.239713.4473
20.4098-0.1436-0.43432.98312.18212.91240.0067-0.1273-0.10640.1470.0513-0.29360.31090.1097-0.0580.0547-0.0079-0.0230.06640.02650.1425-20.8586-16.409340.8077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 317
2X-RAY DIFFRACTION2B30 - 317

+
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