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- PDB-3gc0: Structure of the CMGC CDK Kinase from Giardia lamblia in complex ... -

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Basic information

Entry
Database: PDB / ID: 3gc0
TitleStructure of the CMGC CDK Kinase from Giardia lamblia in complex with AMP
ComponentsKinase, CMGC CDK
KeywordsTRANSFERASE / SSGCID / Kinase / CMGC CDK / AMP / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / : / cyclin binding / phosphorylation / G1/S transition of mitotic cell cycle / regulation of gene expression / signal transduction / ATP binding ...cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / : / cyclin binding / phosphorylation / G1/S transition of mitotic cell cycle / regulation of gene expression / signal transduction / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / 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
ADENOSINE MONOPHOSPHATE / Kinase, CMGC CDK
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of a cyclin-dependent kinase from Giardia lamblia.
Authors: Leibly, D.J. / Newling, P.A. / Abendroth, J. / Guo, W. / Kelley, A. / Stewart, L.J. / Van Voorhis, W.
History
DepositionFeb 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Kinase, CMGC CDK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9242
Polymers37,5771
Non-polymers3471
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.240, 73.180, 75.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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Components

#1: Protein Kinase, CMGC CDK


Mass: 37577.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_8037 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8BZ95
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 290 K / pH: 6.5
Details: 20% PEG 3350, 200MM NA MALONATE, 0.4UL + 0.4UL PROTEIN AT 27 MG/ML, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 20333 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.41 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.44
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / % possible all: 92.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 1oit modified by ccp4 program chainsaw

1oit


Resolution: 2→19.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.597 / SU ML: 0.129 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1029 5.1 %RANDOM
Rwork0.196 ---
obs0.199 20333 99.3 %-
all-20333 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0 Å2
2--2.04 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 23 144 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222287
X-RAY DIFFRACTIONr_bond_other_d0.0010.021563
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9933108
X-RAY DIFFRACTIONr_angle_other_deg0.93933811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25523.04392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64315397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6461516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
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_it1.0921.51401
X-RAY DIFFRACTIONr_mcbond_other0.2381.5558
X-RAY DIFFRACTIONr_mcangle_it1.96222259
X-RAY DIFFRACTIONr_scbond_it2.6433886
X-RAY DIFFRACTIONr_scangle_it4.2924.5847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 60 -
Rwork0.257 1319 -
obs--92.8 %

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