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- PDB-5k28: Structure of the unbound SH3 domain of MLK3 -

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Basic information

Entry
Database: PDB / ID: 5k28
TitleStructure of the unbound SH3 domain of MLK3
ComponentsMitogen-activated protein kinase kinase kinase 11
KeywordsTRANSFERASE / MLK3 / SH3 / phage display / signalling protein
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / microtubule-based process / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity ...mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / microtubule-based process / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / positive regulation of JUN kinase activity / JNK cascade / positive regulation of JNK cascade / RAF activation / small GTPase binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of neuron apoptotic process / MAPK cascade / microtubule / protein autophosphorylation / protein kinase activity / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein homodimerization activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Mainly Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKall, S.K. / Lavie, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification of two distinct peptide-binding pockets in the SH3 domain of human mixed-lineage kinase 3.
Authors: Kokoszka, M.E. / Kall, S.L. / Khosla, S. / McGinnis, J.E. / Lavie, A. / Kay, B.K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 11
B: Mitogen-activated protein kinase kinase kinase 11


Theoretical massNumber of molelcules
Total (without water)13,7992
Polymers13,7992
Non-polymers00
Water2,450136
1
A: Mitogen-activated protein kinase kinase kinase 11


Theoretical massNumber of molelcules
Total (without water)6,9001
Polymers6,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 11


Theoretical massNumber of molelcules
Total (without water)6,9001
Polymers6,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.892, 57.892, 76.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 41 - 102 / Label seq-ID: 1 - 62

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 11 / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase


Mass: 6899.546 Da / Num. of mol.: 2 / Fragment: SH3 domain (UNP residues 44-105)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K11, MLK3, PTK1, SPRK / Production host: Escherichia coli (E. coli)
References: UniProt: Q16584, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 1.4M NaMalonate pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50.14 Å / Num. obs: 23517 / % possible obs: 96.2 % / Redundancy: 4.84 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.79
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.82 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K26

5k26


Resolution: 1.5→50.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.729 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21328 1186 5.1 %RANDOM
Rwork0.18617 ---
obs0.18754 22100 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 0 136 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191006
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9331368
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59223.92251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66415144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.81158
X-RAY DIFFRACTIONr_chiral_restr0.1640.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1581.904511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6292.851637
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6412.272495
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.74417.9311582
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 118 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.24 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 97 -
Rwork0.293 1636 -
obs--99.03 %

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