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- PDB-4c0t: Candida albicans PKh Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 4c0t
TitleCandida albicans PKh Kinase Domain
ComponentsLIKELY PROTEIN KINASE
KeywordsTRANSFERASE / PDK1 ORTHOLOG
Function / homology
Function and homology information


endocytosis / cell cortex / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine/threonine kinase activity / lipid binding / ATP binding / nucleus
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
Serine/threonine-protein kinase PKH2
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsSchulze, J.O. / Pastor-Flores, D. / Biondi, R.M.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: The Pif-Pocket as a Target for C. Albicans Pkh Selective Inhibitors.
Authors: Pastor-Flores, D. / Schulze, J.O. / Bahi, A. / Giacometti, R. / Ferrer-Dalmau, J. / Passeron, S. / Engel, M. / Suess, E. / Casamayor, A. / Biondi, R.M.
History
DepositionAug 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
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_conn
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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIKELY PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)110,0881
Polymers110,0881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.210, 100.210, 60.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein LIKELY PROTEIN KINASE / PKB-ACTIVATING KINASE HOMOLOG


Mass: 110088.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Strain: SC5314
Description: SYNTHETIC GENE BECAUSE CANDIDA HAS NON-UNIVERSAL CODON USAGE
Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q5A3P6, non-specific serine/threonine protein kinase

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.6
Details: 100 MM AMMONIUM SULFATE, 30 % (W/V) PEG 4000, AND 100 MM SODIUM CITRATE/ CITRIC ACID (PH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 30, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.16→70.9 Å / Num. obs: 5590 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Biso Wilson estimate: 53.51 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 14.54
Reflection shellResolution: 3.16→3.26 Å / Redundancy: 8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HRC

3hrc


Resolution: 3.16→70.859 Å / SU ML: 0.45 / σ(F): 2.02 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 280 5 %
Rwork0.228 --
obs0.2305 5590 99.91 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 3.16→70.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 0 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022428
X-RAY DIFFRACTIONf_angle_d0.5933277
X-RAY DIFFRACTIONf_dihedral_angle_d11.272918
X-RAY DIFFRACTIONf_chiral_restr0.046359
X-RAY DIFFRACTIONf_plane_restr0.002416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1602-3.98140.34811360.25972582X-RAY DIFFRACTION100
3.9814-70.8770.24081440.20882728X-RAY DIFFRACTION100

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