[English] 日本語
Yorodumi
- PDB-3epu: Crystal Structure of STM2138, a novel virulence chaperone in Salm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3epu
TitleCrystal Structure of STM2138, a novel virulence chaperone in Salmonella
ComponentsSTM2138 Virulence Chaperone
KeywordsCHAPERONE / Virulence Chaperone / Salmonella / TypeIII Secretion System / STM2138 / SrcA (SsrB-regulated chaperone A)
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #740 / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, K. / Andres, S.N. / Hannemann, M. / Coombes, B. / Junop, M.
CitationJournal: To be Published
Title: Structural analysis and quantitative proteomic interactome of a novel virulence chaperone in Salmonella
Authors: Cooper, C. / Zhang, K. / Andres, S.N. / Hannemann, M. / Junop, M.S. / Coombes, B.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 13, 2013Group: Refinement description
Revision 1.3Sep 6, 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: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone


Theoretical massNumber of molelcules
Total (without water)33,8142
Polymers33,8142
Non-polymers00
Water1,54986
1
A: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone

A: STM2138 Virulence Chaperone
B: STM2138 Virulence Chaperone


Theoretical massNumber of molelcules
Total (without water)67,6284
Polymers67,6284
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8660 Å2
ΔGint-58 kcal/mol
Surface area27650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-18 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.838, 46.832, 65.936
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein STM2138 Virulence Chaperone


Mass: 16906.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: STM2138 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) / References: UniProt: Q8ZNP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane, 200 mM MgCl2, 35% PEG 3350, 3.95 mM FOS-choline-9, 5% (v/v) Jeffamine M-600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2008 / Details: toroidal mirror
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 10664 / Num. obs: 10664 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.62 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.4 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K3E

1k3e


Resolution: 2.5→33.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.719 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 2 TLS GROUPS CORRESPONDS TO THE MAIN CHAIN ATOMS AND THE TLS-3,4 CORRESPONDS TO THE SIDE-CHAINS OF THE SAME RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.25256 538 5 %RANDOM
Rwork0.21448 ---
obs0.21635 10170 99.91 %-
all-10170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.824 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å21.66 Å2
2---0.98 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 86 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222212
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.962992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021686
X-RAY DIFFRACTIONr_nbd_refined0.2240.2878
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.29
X-RAY DIFFRACTIONr_mcbond_it2.3231.51330
X-RAY DIFFRACTIONr_mcangle_it4.11122149
X-RAY DIFFRACTIONr_scbond_it5.0293882
X-RAY DIFFRACTIONr_scangle_it7.4184.5843
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 45 -
Rwork0.27 736 -
obs--100 %
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)
10.5006-0.22670.23180.3441-0.17490.18190.0423-0.08710.0674-0.0582-0.0872-0.01130.0119-0.01020.0449-0.0232-0.00260.01470.0018-0.018-0.051528.01431.86216.0852
20.9625-0.04860.16570.10030.01230.361-0.0124-0.0041-0.01160.01280.01240.0064-0.02-0.01150.00010.0079-0.00260.0167-0.01660.0038-0.026428.10531.683716.1051
30.27150.07050.16370.0846-0.0630.51930.0138-0.05120.02410.0289-0.07020.01320.05460.02330.0565-0.0561-0.01350.0132-0.01680.0019-0.02325.1271-4.27711.0072
40.2070.0580.06730.0653-0.05770.14120.013-0.040.00230.0352-0.0118-0.00080.0066-0.0337-0.0011-0.00150.01210.01460.0021-0.004-0.01595.0286-4.41611.0814
50.00520.0042-0.02830.0034-0.0230.1546-0.0724-0.0197-0.02520.03230.07840.04150.0184-0.0787-0.00610.0236-0.0074-0.00590.07530.02520.059714.5171-3.295312.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 136
2X-RAY DIFFRACTION2A1 - 136
3X-RAY DIFFRACTION3B3 - 135
4X-RAY DIFFRACTION4B3 - 135
5X-RAY DIFFRACTION5B1 - 230

+
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