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- PDB-4xhh: Structure of C. glabrata Hrr25, Apo state -

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Basic information

Entry
Database: PDB / ID: 4xhh
TitleStructure of C. glabrata Hrr25, Apo state
ComponentsSimilar to uniprot|P29295 Saccharomyces cerevisiae YPL204w HRR25
KeywordsTRANSFERASE / casein kinase / monopolin
Function / homology
Function and homology information


regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / tRNA wobble uridine modification / cellular bud tip / cellular bud neck / regulation of autophagosome assembly ...regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / tRNA wobble uridine modification / cellular bud tip / cellular bud neck / regulation of autophagosome assembly / pexophagy / spindle pole body / preribosome, small subunit precursor / ribosomal large subunit biogenesis / P-body / ribosomal small subunit biogenesis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / DNA repair / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
PHOSPHATE ION / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104141 United States
CitationJournal: Embo J. / Year: 2016
Title: Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator.
Authors: Ye, Q. / Ur, S.N. / Su, T.Y. / Corbett, K.D.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Similar to uniprot|P29295 Saccharomyces cerevisiae YPL204w HRR25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4158
Polymers46,7501
Non-polymers6657
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.091, 77.860, 85.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Similar to uniprot|P29295 Saccharomyces cerevisiae YPL204w HRR25


Mass: 46750.430 Da / Num. of mol.: 1 / Fragment: UNP residues 1-403 / Mutation: K38R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FS46
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.1 M CAPS pH 10.5, 0.2 M lithium sulfate, 0.56 M NaH2PO4, 0.66 M K2HPO4
PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.89→85.08 Å / Num. obs: 11067 / % possible obs: 98.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.273 / Net I/σ(I): 10.8
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XH0

4xh0


Resolution: 2.908→57.438 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 548 5.06 %
Rwork0.2032 --
obs0.2043 10836 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.908→57.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 35 41 3025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053043
X-RAY DIFFRACTIONf_angle_d0.84091
X-RAY DIFFRACTIONf_dihedral_angle_d14.21142
X-RAY DIFFRACTIONf_chiral_restr0.034429
X-RAY DIFFRACTIONf_plane_restr0.003512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9079-3.20050.26771200.25532398X-RAY DIFFRACTION94
3.2005-3.66360.2481430.20712568X-RAY DIFFRACTION100
3.6636-4.61540.19141570.17282586X-RAY DIFFRACTION100
4.6154-57.44910.22981280.20752736X-RAY DIFFRACTION100
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)
11.8843-0.6771-0.26921.91620.28821.5717-0.1288-0.31680.32770.01820.09920.456-0.4089-0.55530.07660.38770.1003-0.01450.4509-0.02820.375212.9924-25.097510.9419
22.1351-0.33280.44391.18990.00811.4773-0.1470.16630.4202-0.0570.0642-0.1183-0.2369-0.03590.0280.2041-0.0004-0.03240.23010.02740.232325.564-26.3035-14.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 397 )

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