[English] 日本語
Yorodumi
- PDB-2bsj: Native Crystal Structure of the Type III Secretion chaperone SycT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bsj
TitleNative Crystal Structure of the Type III Secretion chaperone SycT from Yersinia enterocolitica
ComponentsCHAPERONE PROTEIN SYCT
KeywordsCHAPERONE / TYPE III SECRETION / YERSINIA / EFFECTOR / YOPT
Function / homologyTir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / protein secretion by the type III secretion system / 2-Layer Sandwich / Alpha Beta / Chaperone protein SycT / Chaperone protein SycT
Function and homology information
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsButtner, C.R. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal Structure of Yersinia Enterocolitica Type III Secretion Chaperone Syct.
Authors: Buttner, C.R. / Cornelis, G.R. / Heinz, D.W. / Niemann, H.H.
History
DepositionMay 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 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: CHAPERONE PROTEIN SYCT
B: CHAPERONE PROTEIN SYCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7814
Polymers30,7102
Non-polymers712
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)34.112, 79.562, 52.093
Angle α, β, γ (deg.)90.00, 101.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.96012, -0.26736, -0.08175), (-0.26376, 0.76925, 0.58197), (-0.09271, 0.58033, -0.80909)
Vector: 3.17197, -9.49084, 28.78245)

-
Components

#1: Protein CHAPERONE PROTEIN SYCT


Mass: 15355.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703
Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227
Plasmid: PET-M-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O85243, UniProt: P0C2V9*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.26 Å3/Da / Density % sol: 46 %
Description: NATIVE SYCT STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH 2BSH AND 2BSI
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M SODIUM CITRATE PH 5.6, 5 % ISOPROPANOL, 21 % POLYETHYLENE GLYCOL 4000, HANGING-DROP VAPOR DIFFUSION AT 4 DEGREE CELSIUS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.83→79.5 Å / Num. obs: 23529 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 83.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2BSH, 2BSI

2bsh

2bsi


Resolution: 1.83→79.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.498 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1185 5 %RANDOM
Rwork0.184 ---
obs0.186 22341 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.74 Å2
2---0.86 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.83→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 2 168 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9252977
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5226.032126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.915156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021730
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21506
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.51334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61122093
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4113982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.564.5884
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 68 -
Rwork0.234 1475 -
obs--85.3 %
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)
11.98790.92620.92771.60791.24511.48310.0522-0.3301-0.08250.1768-0.05380.00680.0351-0.08550.0016-0.00030.01510.02090.01760.022-0.07526.808-21.306119.5094
21.8156-0.43090.26511.9744-0.91740.8618-0.00470.08550.0471-0.05630.04790.027-0.0119-0.0297-0.0432-0.06650.00110.0146-0.06580.0024-0.0793-0.2578-15.31840.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 130
2X-RAY DIFFRACTION2B2 - 117
3X-RAY DIFFRACTION2B125 - 130

+
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