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- PDB-2dyl: Crystal structure of human mitogen-activated protein kinase kinas... -

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Basic information

Entry
Database: PDB / ID: 2dyl
TitleCrystal structure of human mitogen-activated protein kinase kinase 7 activated mutant (S287D, T291D)
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / MKK7 / kinase / activated mutant / ATP-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / phosphorylation / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 Å
AuthorsKukimoto-Niino, M. / Takagi, T. / Kaminishi, T. / Uchikubo-Kamo, T. / Terada, T. / Matsuzaki, O. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human mitogen-activated protein kinase kinase 7 activated mutant (S287D, T291D)
Authors: Kukimoto-Niino, M. / Takagi, T. / Kaminishi, T. / Uchikubo-Kamo, T. / Terada, T. / Matsuzaki, O. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 7


Theoretical massNumber of molelcules
Total (without water)35,7601
Polymers35,7601
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.552, 69.635, 84.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 7 / mitogen-activated protein kinase kinase 7 gamma 1 / MAP kinase kinase 7 / MAPKK 7 / MAPK/ERK kinase ...mitogen-activated protein kinase kinase 7 gamma 1 / MAP kinase kinase 7 / MAPKK 7 / MAPK/ERK kinase 7 / JNK-activating kinase 2 / c-Jun N-terminal kinase kinase 2 / JNK kinase 2 / JNKK 2


Mass: 35760.262 Da / Num. of mol.: 1 / Fragment: Kinase domain, residues 101-405 / Mutation: S287D, T291D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Plasmid: PX060911-21
References: UniProt: O14733, mitogen-activated protein kinase kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 0.2M ammonium acetate, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 13708 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.77064 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 26.0099
Reflection shellResolution: 2.45→2.54 Å / Mean I/σ(I) obs: 2.95349 / Rsym value: 0.477 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1S9J

1s9j


Resolution: 2.45→46.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1155116.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 1391 10.2 %RANDOM
Rwork0.217 ---
obs0.217 13670 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5177 Å2 / ksol: 0.358748 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å20 Å2
2--8.55 Å20 Å2
3----5.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.45→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 37 2233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 247 11.3 %
Rwork0.277 1947 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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