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- PDB-4agu: CRYSTAL STRUCTURE OF THE HUMAN CDKL1 KINASE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 4agu
TitleCRYSTAL STRUCTURE OF THE HUMAN CDKL1 KINASE DOMAIN
ComponentsCYCLIN-DEPENDENT KINASE-LIKE 1
KeywordsTRANSFERASE / PHOSPHO-MIMETIC / KINASE
Function / homology
Function and homology information


ciliary transition zone / regulation of cilium assembly / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / heart development / protein phosphorylation / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / ATP binding ...ciliary transition zone / regulation of cilium assembly / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / heart development / protein phosphorylation / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / ATP binding / nucleus / 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, 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-D15 / Cyclin-dependent kinase-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCanning, P. / Sharpe, T.D. / Allerston, C. / Savitsky, P. / Pike, A.C.W. / Muniz, J.R.C. / Chaikuad, A. / Kuo, K. / Burgess-Brown, N. / Ayinampudi, V. ...Canning, P. / Sharpe, T.D. / Allerston, C. / Savitsky, P. / Pike, A.C.W. / Muniz, J.R.C. / Chaikuad, A. / Kuo, K. / Burgess-Brown, N. / Ayinampudi, V. / Zhang, Y. / Thangaratnarajah, C. / Ugochukwu, E. / Vollmar, M. / Krojer, T. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Knapp, S. / Bullock, A.
CitationJournal: Cell Rep / Year: 2018
Title: CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.
Authors: Canning, P. / Park, K. / Goncalves, J. / Li, C. / Howard, C.J. / Sharpe, T.D. / Holt, L.J. / Pelletier, L. / Bullock, A.N. / Leroux, M.R.
History
DepositionJan 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 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 1.2Mar 30, 2022Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _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
Revision 1.3Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE-LIKE 1
B: CYCLIN-DEPENDENT KINASE-LIKE 1
C: CYCLIN-DEPENDENT KINASE-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2646
Polymers108,9213
Non-polymers1,3443
Water5,675315
1
A: CYCLIN-DEPENDENT KINASE-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7552
Polymers36,3071
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYCLIN-DEPENDENT KINASE-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7552
Polymers36,3071
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYCLIN-DEPENDENT KINASE-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7552
Polymers36,3071
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.980, 123.980, 49.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5314, 0.8471, 0.009), (-0.847, -0.5315, 0.0059), (0.0098, -0.0045, 0.9999)-59.4174, 183.6634, -4.5954
2given(-0.4916, -0.8704, 0.0276), (0.8708, -0.4916, 0.0068), (0.0077, 0.0274, 0.9996)124.3537, 142.8046, 1.9274

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Components

#1: Protein CYCLIN-DEPENDENT KINASE-LIKE 1


Mass: 36306.891 Da / Num. of mol.: 3 / Fragment: KINASE DOMAIN, RESIDUES 1-300 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 PRARE2 / References: UniProt: Q00532
#2: Chemical ChemComp-D15 / N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide


Mass: 447.917 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H22ClN5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU ENGINEERED RESIDUE IN CHAIN B, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN B, TYR 161 TO GLU ENGINEERED RESIDUE IN CHAIN C, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN C, TYR 161 TO GLU
Sequence detailsCONFLICT Q274E IS A DOCUMENTED NATURAL VARIANT. CONFLICT A152 AND N301D ARE DOCUMENTED SEQUENCE ...CONFLICT Q274E IS A DOCUMENTED NATURAL VARIANT. CONFLICT A152 AND N301D ARE DOCUMENTED SEQUENCE CONFLICTS. CONTAINS TWO PHOSPHO-MIMETIC ACTIVATING MUTATIONS, Y161E AND T159D.

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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: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 17.5% PEG 3350, 0.1 M (NH4)CL PH 6.3, 0.05 M MG FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.4→29.78 Å / Num. obs: 33165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 54.57 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AAA

4aaa


Resolution: 2.4→29.78 Å / Cor.coef. Fo:Fc: 0.9582 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.446 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.245
Details: RESIDUES 152-163 OF CHAIN A AND RESIDUE 39-40 OF CHAIN B ARE DISORDERED. IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NCS REPRESENTATION IS RESTRAINT LSSR (- ...Details: RESIDUES 152-163 OF CHAIN A AND RESIDUE 39-40 OF CHAIN B ARE DISORDERED. IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NCS REPRESENTATION IS RESTRAINT LSSR (-AUTONCS). NUMBER OF RESTRAIN LIBRARIES USED 9.
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1676 5.06 %RANDOM
Rwork0.1865 ---
obs0.1885 33152 99.98 %-
Displacement parametersBiso mean: 60.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.823 Å20 Å20 Å2
2--1.823 Å20 Å2
3----3.6459 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 96 315 6810
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016673HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039093HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2983SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes984HARMONIC5
X-RAY DIFFRACTIONt_it6673HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion869SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7634SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2461 127 4.35 %
Rwork0.2 2792 -
all0.202 2919 -
obs--99.98 %
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)
12.20450.6197-0.04184.12650.96061.8869-0.2934-0.083-0.0202-0.04170.04570.43660.0572-0.33780.2477-0.1903-0.00970.0115-0.1486-0.0473-0.116242.4489102.6769-1.5262
25.39320.3891-0.83141.7727-0.03151.1488-0.19810.1849-0.36740.20560.0127-0.10010.32430.25970.1854-0.17490.07140.0761-0.18990.0248-0.10314.5105129.4483.2681
33.8505-1.34691.75942.8641-0.86282.214-0.01670.00820.5270.03980.0235-0.1805-0.29780.0891-0.0069-0.1531-0.01250.0753-0.19260.0248-0.09125.204390.8823-6.348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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