[English] 日本語
Yorodumi
- PDB-5m43: Crystal structure of Yvh1 phosphatase domain from Chaetomium ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m43
TitleCrystal structure of Yvh1 phosphatase domain from Chaetomium thermophilum
ComponentsPutative uncharacterized protein
KeywordsRIBOSOME / phosphatase
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.646 Å
AuthorsAhmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Protein Sci. / Year: 2017
Title: Interaction network of the ribosome assembly machinery from a eukaryotic thermophile.
Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. ...Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. / Thomson, E. / Flemming, D. / Sinning, I. / Hurt, E.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9595
Polymers25,6511
Non-polymers3084
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint2 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.758, 88.758, 53.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

-
Components

#1: Protein Putative uncharacterized protein


Mass: 25650.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495
Gene: CTHT_0021070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S3H6
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiNO3 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.646→45.55 Å / Num. obs: 25830 / % possible obs: 98.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.6
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.62 / CC1/2: 0.916 / % possible all: 93.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.634
Highest resolutionLowest resolution
Rotation45.56 Å1.89 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
MOLREPphasing
PHENIX(1.10.1_2155: ???refinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRM

1wrm


Resolution: 1.646→44.379 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.1868 1363 5.28 %
Rwork0.1631 --
obs0.1644 25797 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.39 Å2 / Biso mean: 33.5755 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 1.646→44.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 20 222 1577
Biso mean--47.27 47.3 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171419
X-RAY DIFFRACTIONf_angle_d1.3731917
X-RAY DIFFRACTIONf_chiral_restr0.103207
X-RAY DIFFRACTIONf_plane_restr0.01249
X-RAY DIFFRACTIONf_dihedral_angle_d15.822849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6457-1.70450.24331460.20422298244495
1.7045-1.77280.20821330.19222387252098
1.7728-1.85350.2261190.17152399251898
1.8535-1.95120.16281400.15932403254398
1.9512-2.07340.16921100.15752438254898
2.0734-2.23350.17851300.14872436256698
2.2335-2.45830.20621410.1572436257799
2.4583-2.81390.18411570.1712456261399
2.8139-3.5450.16661420.16122525266799
3.545-44.39510.19331450.160926562801100
Refinement TLS params.Method: refined / Origin x: 22.4859 Å / Origin y: -0.3732 Å / Origin z: -9.4046 Å
111213212223313233
T0.1142 Å20.0046 Å20.0068 Å2-0.1175 Å2-0.0487 Å2--0.3369 Å2
L1.9943 °20.9866 °20.6377 °2-3.0795 °21.0163 °2--1.9839 °2
S-0.0457 Å °-0.082 Å °0.1212 Å °-0.102 Å °0.1164 Å °-0.2489 Å °-0.1513 Å °0.0045 Å °-0.0113 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 175
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 202
5X-RAY DIFFRACTION1allS203 - 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