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- PDB-3vn9: Rifined Crystal structure of non-phosphorylated MAP2K6 in a putat... -

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Basic information

Entry
Database: PDB / ID: 3vn9
TitleRifined Crystal structure of non-phosphorylated MAP2K6 in a putative auto-inhibition state
ComponentsDual specificity mitogen-activated protein kinase kinase 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / auto-inhibition state / activation helices / Mitogen-activated protein kinase kinase / AMP-PNP binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cellular response to sorbitol / ovulation cycle process / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of prostaglandin secretion / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / positive regulation of nitric-oxide synthase biosynthetic process / p38MAPK cascade ...cellular response to sorbitol / ovulation cycle process / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of prostaglandin secretion / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / positive regulation of nitric-oxide synthase biosynthetic process / p38MAPK cascade / PI5P Regulates TP53 Acetylation / MAP kinase kinase activity / Uptake and function of anthrax toxins / signal transduction in response to DNA damage / cardiac muscle contraction / stress-activated MAPK cascade / regulation of signal transduction by p53 class mediator / activated TAK1 mediates p38 MAPK activation / response to ischemia / NOD1/2 Signaling Pathway / bone development / PKR-mediated signaling / Interleukin-1 signaling / osteoblast differentiation / MAPK cascade / cellular senescence / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / positive regulation of MAPK cascade / cytoskeleton / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of protein phosphorylation / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
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, ATP binding site / Protein kinases ATP-binding region signature. ...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, ATP binding site / Protein kinases ATP-binding region signature. / 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
Chem-ANK / Dual specificity mitogen-activated protein kinase kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKinoshita, T. / Matsuzaka, H. / Nakai, R. / Kirii, Y. / Yokota, K. / Tada, T. / Matsumoto, T.
CitationJournal: J.Biochem. / Year: 2012
Title: Crystal structure of non-phosphorylated MAP2K6 in a putative auto-inhibition state
Authors: Matsumoto, T. / Kinoshita, T. / Matsuzaka, H. / Nakai, R. / Kirii, Y. / Yokota, K. / Tada, T.
History
DepositionJan 5, 2012Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 29, 2012ID: 3AN0
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,3691
Non-polymers5312
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.456, 83.456, 101.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 6 / MAP kinase kinase 6 / MAPKK 6 / MAPK/ERK kinase 6 / MEK 6 / Stress-activated protein kinase kinase ...MAP kinase kinase 6 / MAPKK 6 / MAPK/ERK kinase 6 / MEK 6 / Stress-activated protein kinase kinase 3 / SAPK kinase 3 / SAPKK-3 / SAPKK3


Mass: 38369.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K6 / Plasmid: PET22(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P52564, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-ANK / 9-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-beta-L-ribofuranosyl}-9H-purin-6-amine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG4000, 10% 2-propanol, 0.1mol/L Na-HEPES-HCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 28, 2010 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12124 / Num. obs: 12124 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.26 % / Rmerge(I) obs: 0.124
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.72 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eqd

3eqd


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.123 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 1207 10 %RANDOM
Rwork0.26366 ---
all0.26526 10917 --
obs0.26526 10917 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 98.389 Å2
Baniso -1Baniso -2Baniso -3
1-4.88 Å22.44 Å2-0 Å2
2--4.88 Å2-0 Å2
3----7.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 32 18 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022354
X-RAY DIFFRACTIONr_angle_refined_deg2.5941.993194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09924.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.0315416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.967159
X-RAY DIFFRACTIONr_chiral_restr0.1450.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211728
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 80 -
Rwork0.443 771 -
obs--100 %

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