[English] 日本語
Yorodumi
- PDB-5yyx: Crystal Structure of the MEK1 FHA domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yyx
TitleCrystal Structure of the MEK1 FHA domain
ComponentsMeiosis-specific serine/threonine-protein kinase MEK1
KeywordsTRANSFERASE / Meiosis / Forkhead-associatedd domain / Regulatory Motif.
Function / homology
Function and homology information


meiotic recombination checkpoint signaling / meiotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Meiosis-specific serine/threonine-protein kinase MEK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 Å
AuthorsXie, C. / Li, F. / Jiang, Y. / Wu, J. / Shi, Y.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural insights into the recognition of phosphorylated Hop1 by Mek1
Authors: Xie, C. / He, C. / Jiang, Y. / Yu, H. / Cheng, L. / Nshogoza, G. / Ala, M.S. / Tian, C. / Wu, J. / Shi, Y. / Li, F.
History
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Nov 22, 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: Meiosis-specific serine/threonine-protein kinase MEK1


Theoretical massNumber of molelcules
Total (without water)16,1071
Polymers16,1071
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7040 Å2
Unit cell
Length a, b, c (Å)61.666, 61.666, 61.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

-
Components

#1: Protein Meiosis-specific serine/threonine-protein kinase MEK1


Mass: 16107.298 Da / Num. of mol.: 1 / Fragment: UNP residues 20-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MEK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P24719, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% PEG8000, 0.1M Imidazole malate pH7.5, 1.0M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97736 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 15632 / % possible obs: 99.4 % / Redundancy: 19.4 % / Biso Wilson estimate: 19.64 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.019 / Rrim(I) all: 0.084 / Χ2: 0.573 / Net I/σ(I): 4.7 / Num. measured all: 303239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.7218.30.5899360.9510.140.6060.45391.1
1.72-1.7620.10.4610360.9750.1050.4720.452100
1.76-1.8120.10.37310430.9810.0850.3830.473100
1.81-1.8619.70.28710120.9870.0660.2950.478100
1.86-1.92190.24310360.990.0570.250.517100
1.92-1.9918.80.19110290.9930.0450.1970.516100
1.99-2.0720.40.16810330.9950.0380.1730.554100
2.07-2.17200.13110510.9970.030.1340.557100
2.17-2.2819.40.11710440.9980.0270.120.581100
2.28-2.4218.60.10110320.9980.0240.1040.542100
2.42-2.6120.20.09110460.9980.0210.0930.577100
2.61-2.8719.80.0810490.9980.0180.0820.616100
2.87-3.29190.06710590.9990.0160.0690.694100
3.29-4.1419.70.05810920.9990.0130.060.815100
4.14-5017.90.05111340.9990.0120.0530.741100

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6G

1g6g


Resolution: 1.684→40.204 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 792 5.07 %
Rwork0.1827 14815 -
obs0.1847 15607 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.71 Å2 / Biso mean: 25.7348 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.684→40.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 82 1048
Biso mean---36.47 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061013
X-RAY DIFFRACTIONf_angle_d0.9061376
X-RAY DIFFRACTIONf_chiral_restr0.059160
X-RAY DIFFRACTIONf_plane_restr0.005171
X-RAY DIFFRACTIONf_dihedral_angle_d12.948612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6839-1.78940.2461370.225924122549
1.7894-1.92750.22461480.185224372585
1.9275-2.12150.20021160.176124542570
2.1215-2.42840.23761250.182724432568
2.4284-3.05940.20831290.19724882617
3.0594-40.2150.23231370.171925812718
Refinement TLS params.Method: refined / Origin x: 7.1292 Å / Origin y: 36.4223 Å / Origin z: 7.768 Å
111213212223313233
T0.1095 Å20.0067 Å2-0.001 Å2-0.1178 Å20.0023 Å2--0.0995 Å2
L2.5084 °2-0.083 °2-0.2325 °2-2.5815 °2-0.1372 °2--2.2908 °2
S0.006 Å °-0.1356 Å °-0.0121 Å °0.1086 Å °0.0258 Å °0.0096 Å °0.0226 Å °-0.12 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 137
2X-RAY DIFFRACTION1allC2 - 64
3X-RAY DIFFRACTION1allC66 - 82
4X-RAY DIFFRACTION1allC83 - 97
5X-RAY DIFFRACTION1allC98 - 99
6X-RAY DIFFRACTION1allC100 - 104
7X-RAY DIFFRACTION1allC105 - 107

+
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