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- PDB-4aw2: Crystal structure of CDC42 binding protein kinase alpha (MRCK alpha) -

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Basic information

Entry
Database: PDB / ID: 4aw2
TitleCrystal structure of CDC42 binding protein kinase alpha (MRCK alpha)
ComponentsSERINE/THREONINE-PROTEIN KINASE MRCK ALPHA
KeywordsTRANSFERASE / CDC42BPA
Function / homology
Function and homology information


: / actomyosin / actomyosin structure organization / nuclear migration / regulation of small GTPase mediated signal transduction / cell leading edge / cytoskeleton organization / peptidyl-threonine phosphorylation / microtubule cytoskeleton organization / cell-cell junction ...: / actomyosin / actomyosin structure organization / nuclear migration / regulation of small GTPase mediated signal transduction / cell leading edge / cytoskeleton organization / peptidyl-threonine phosphorylation / microtubule cytoskeleton organization / cell-cell junction / cell migration / lamellipodium / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase MRCK alpha / KELK-motif containing domain / KELK-motif containing domain of MRCK Ser/Thr protein kinase / Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / CRIB domain profile. ...Serine/threonine-protein kinase MRCK alpha / KELK-motif containing domain / KELK-motif containing domain of MRCK Ser/Thr protein kinase / Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 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-22E / Serine/threonine-protein kinase MRCK alpha
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsElkins, J.M. / Muniz, J.R.C. / Tan, I. / Leung, T. / Lafanechere, L. / Prudent, R. / Abdul Azeez, K. / Szklarz, M. / Phillips, C. / Wang, J. ...Elkins, J.M. / Muniz, J.R.C. / Tan, I. / Leung, T. / Lafanechere, L. / Prudent, R. / Abdul Azeez, K. / Szklarz, M. / Phillips, C. / Wang, J. / von Delft, F. / Bountra, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Cdc42 Binding Protein Kinase Alpha (Mrck Alpha)
Authors: Elkins, J.M. / Muniz, J.R.C. / Tan, I. / Leung, T. / Lafanechere, L. / Prudent, R. / Abdul Azeez, K. / Szklarz, M. / Phillips, C. / Wang, J. / von Delft, F. / Bountra, C. / Edwards, A. / Knapp, S.
History
DepositionMay 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SERINE/THREONINE-PROTEIN KINASE MRCK ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9036
Polymers50,2721
Non-polymers6315
Water3,801211
1
A: SERINE/THREONINE-PROTEIN KINASE MRCK ALPHA
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE MRCK ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,80512
Polymers100,5442
Non-polymers1,26110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7380 Å2
ΔGint-15.1 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.744, 49.187, 97.762
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE MRCK ALPHA / CDC42-BINDING PROTEIN KINASE ALPHA / MYOTONIC DYSTROPHY KINASE-RELATED CDC42-BINDING KINASE ALPHA / ...CDC42-BINDING PROTEIN KINASE ALPHA / MYOTONIC DYSTROPHY KINASE-RELATED CDC42-BINDING KINASE ALPHA / MRCK ALPHA / MYOTONIC DYSTROPHY PROTEIN KINASE-LIKE ALPHA CDC42 BINDING PROTEIN KINASE ALPHA


Mass: 50271.879 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 2-424 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PNIC-CTH0 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O54874, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-22E / 5,11-dimethyl-1-oxo-2,6-dihydro-1h-pyrido[4,3-b]carbazol-9-yl benzoate


Mass: 382.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18N2O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 254 TO GLY

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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: 2.34 Å3/Da / Density % sol: 47.44 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M KSCN, 0.1M BISTRISPROPANE PH 8.5, 20% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.7→28.91 Å / Num. obs: 49832 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VD5

2vd5


Resolution: 1.7→89.72 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.183 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19326 2038 4.1 %RANDOM
Rwork0.16923 ---
obs0.17022 47784 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.425 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-0.59 Å2
2--2.8 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→89.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 45 211 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023345
X-RAY DIFFRACTIONr_bond_other_d0.0010.022290
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9694528
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0015554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03324.049163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.251522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02710
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 143 -
Rwork0.296 7187 -
obs--96.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8378-0.5721-0.00811.3730.539910.8755-0.0086-0.00810.13840.1037-0.07780.1228-0.3044-0.56120.08640.10380.07930.00260.1296-0.0310.1125-7.93823.016-9.055
22.5463-0.5232-1.2251.04030.8145.3025-0.0437-0.0864-0.41330.08-0.09290.01050.67290.52390.13660.13810.04620.00080.10050.02910.09475.5596.924.426
32.7446-0.1871-0.39470.91910.51171.70220.0578-0.253-0.18890.1238-0.05120.02460.1032-0.0413-0.00650.1082-0.05960.00610.06120.02720.0356-9.06112.96722.274
42.83150.2591-0.33181.24460.23871.79960.01950.0684-0.0455-0.0284-0.0290.1674-0.0709-0.25270.00950.08740.0116-0.01850.08640.02690.0692-34.44416.51425.156
57.0347-2.95683.74531.6763-1.45143.9395-0.0952-0.07390.55890.022-0.0853-0.0571-0.23180.08950.18040.2618-0.06280.02630.1232-0.02570.1911-20.06228.53433.033
63.42462.0183-0.72655.1682-0.53114.06320.02820.15710.0362-0.09050.0096-0.0087-0.1604-0.1779-0.03780.0433-0.00980.00360.0474-0.01070.0099-6.22816.0768.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 73
3X-RAY DIFFRACTION3A74 - 157
4X-RAY DIFFRACTION4A158 - 346
5X-RAY DIFFRACTION5A347 - 392
6X-RAY DIFFRACTION6A393 - 417

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