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- PDB-2c30: Crystal Structure Of The Human P21-Activated Kinase 6 -

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Basic information

Entry
Database: PDB / ID: 2c30
TitleCrystal Structure Of The Human P21-Activated Kinase 6
ComponentsSERINE/THREONINE-PROTEIN KINASE PAK 6
KeywordsTRANSFERASE / CRIB DOMAIN / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RAC1 GTPase cycle / cytoskeleton organization ...neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RAC1 GTPase cycle / cytoskeleton organization / cellular response to starvation / learning / locomotory behavior / memory / fibrillar center / cell junction / non-specific serine/threonine protein kinase / postsynaptic density / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase PAK 6 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Serine/threonine-protein kinase PAK 6 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase 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
PHOSPHATE ION / Serine/threonine-protein kinase PAK 6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFilippakopoulos, P. / Berridge, G. / Bray, J. / Burgess, N. / Colebrook, S. / Das, S. / Eswaran, J. / Gileadi, O. / Papagrigoriou, E. / Savitsky, P. ...Filippakopoulos, P. / Berridge, G. / Bray, J. / Burgess, N. / Colebrook, S. / Das, S. / Eswaran, J. / Gileadi, O. / Papagrigoriou, E. / Savitsky, P. / Smee, C. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S.
CitationJournal: Structure / Year: 2007
Title: Crystal Structures of the P21-Activated Kinases Pak4, Pak5, and Pak6 Reveal Catalytic Domain Plasticity of Active Group II Paks.
Authors: Eswaran, J. / Lee, W.H. / Debreczeni, J.E. / Filippakopoulos, P. / Turnbull, A. / Fedorov, O. / Deacon, S.W. / Peterson, J.R. / Knapp, S.
History
DepositionOct 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8103
Polymers36,6791
Non-polymers1302
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.781, 66.674, 96.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PAK 6 / P21-ACTIVATED KINASE 6 / PAK-6 / PAK-5


Mass: 36679.270 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 383-681
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9NQU5, EC: 2.7.1.37
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 51.68 %
Description: ENSEMBLE OF MODELS WAS USED IN PHASER AS SEARCH MODEL.
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 1.60M MGSO4 0.1M MES PH 6.5 SITTING DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.6→55 Å / Num. obs: 177870 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M

2bva

1yhw

1yhv

1f3m


Resolution: 1.6→54.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.633 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. UNEXPLAINED SIGMAA DENSITY REMAINS UNMODELLED AFTER THE LAST MODELLED RESIDUE, AND AROUND SIDECHAIN A615.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1675 3.3 %RANDOM
Rwork0.197 ---
obs0.198 49551 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 6 350 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222384
X-RAY DIFFRACTIONr_bond_other_d0.0020.021
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9873234
X-RAY DIFFRACTIONr_angle_other_deg0.04632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02923.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415.034446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0831519
X-RAY DIFFRACTIONr_chiral_restr0.1190.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021
X-RAY DIFFRACTIONr_nbd_refined0.2120.21220
X-RAY DIFFRACTIONr_nbd_other0.0070.21
X-RAY DIFFRACTIONr_nbtor_refined0.310.21670
X-RAY DIFFRACTIONr_nbtor_other0.2720.22
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2211.51499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60122382
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5313986
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9054.5851
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 112
Rwork0.278 3264
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)
10.6901-0.459-0.31761.03680.340.96010.04960.0531-0.0185-0.0556-0.00320.0643-0.0732-0.0264-0.0464-0.0628-0.00820.019-0.0232-0.0067-0.048550.30354.0933-2.3532
21.1612-0.1002-0.2141.1720.10530.9937-0.0092-0.0766-0.05060.07360.0034-0.00570.04840.05190.0058-0.089-0.0140.0087-0.0902-0.0164-0.105738.366855.156921.6948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A385 - 485
2X-RAY DIFFRACTION2A486 - 674

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