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- PDB-5yyx: Crystal Structure of the MEK1 FHA domain -

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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 / HSF1-dependent transactivation / calcium/calmodulin-dependent protein kinase activity / meiotic cell cycle / cellular response to oxidative stress / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...meiotic recombination checkpoint signaling / HSF1-dependent transactivation / calcium/calmodulin-dependent protein kinase activity / meiotic cell cycle / cellular response to oxidative stress / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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

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