[English] 日本語
Yorodumi
- PDB-1k46: Crystal Structure of the Type III Secretory Domain of Yersinia Yo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k46
TitleCrystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer
ComponentsPROTEIN-TYROSINE PHOSPHATASE YOPH
KeywordsHYDROLASE / domain-swap / phosphopeptide-binding domain / type III secretion domain
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsSmith, C.L. / Khandelwal, P. / Keliikuli, K. / Zuiderweg, E.R.P. / Saper, M.A.
Citation
Journal: Mol.Microbiol. / Year: 2001
Title: Structure of the type III secretion and substrate-binding domain of Yersinia YopH phosphatase.
Authors: Smith, C.L. / Khandelwal, P. / Keliikuli, K. / Zuiderweg, E.R. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Identification of Residues in the N-terminal Domain of the Yersinia Tyrosine Phosphatase that are Critical for Substrate Recognition
Authors: Montagna, L.G. / Ivanov, M.I. / Bliska, J.B.
#2: Journal: Mol.Microbiol. / Year: 1998
Title: Identification of an Amino-terminal Substrate-binding Domain in the Yersinia Tyrosine Phosphatase that is Required for Efficient Recognition of Focal Adhesion Targets
Authors: Black, D.S. / Montagna, L.G. / Zitsmann, S. / Bliska, J.B.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THIS IS LIKELY THE BIOLOGICALLY-RELEVANT STRUCTURE. THE RELEVANCE OF THE DOMAIN-SWAPPED DIMER OBSERVED IN THE CRYSTAL STRUCTURE IS DESCRIBED IN THE JRNL REFERENCE. ALSO SEE REMARK 900. THE OTHER MOLECULE OF THE DOMAIN-SWAPPED DIMER IS GENERATED BY APPLYING CRYSTALLOGRAPHIC OPERATOR 3 IN REMARK 290 FOLLOWED BY A TRANSLATION OF 47.90 IN X.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE YOPH


Theoretical massNumber of molelcules
Total (without water)14,8831
Polymers14,8831
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN-TYROSINE PHOSPHATASE YOPH

A: PROTEIN-TYROSINE PHOSPHATASE YOPH


Theoretical massNumber of molelcules
Total (without water)29,7652
Polymers29,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5070 Å2
ΔGint-34 kcal/mol
Surface area12080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.900, 120.700, 48.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsYopH(1-129) can exist as a monomer or dimer in solution. Crystal structure is a domain-swapped dimer consisting of two molecules related by a crystallographic two fold axis: -x+1,y,-z+1/2. The physiologically-relevant form is likely the monomer.

-
Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE YOPH / YopH phosphatase


Mass: 14882.599 Da / Num. of mol.: 1 / Fragment: amino-terminal domain (residues 1-129)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: yopH / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08538, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, sodium chlolride, Tris , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropNaCl
21 mMEDTA1drop
30.1 %beta-mercaptoethanol1drop
410 mMimidazole1droppH7.2
510 mg/mlprotein1drop
62-10 %PEG80001reservoir
790-100 mM1reservoirNaCl
8100 mMTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 1998 / Details: mirrors
RadiationMonochromator: Yale double focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22 Å / Num. all: 7503 / Num. obs: 7503 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 16.2 / Num. unique all: 720 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 68285 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 720

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: de novo

Resolution: 2.2→22 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 747 -random
Rwork0.224 ---
all-7479 --
obs-7479 100 %-
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 110 1054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.115
LS refinement shellResolution: 2.2→2.25 Å
RfactorNum. reflection
Rfree0.2757 49
Rwork0.222 -
obs-461
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22 Å / σ(F): 0 / Rfactor obs: 0.224 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
LS refinement shell
*PLUS
Rfactor Rwork: 0.222 / Rfactor obs: 0.222

+
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