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- PDB-4xhg: Structure of C. glabrata Hrr25 bound to ADP (formate condition) -

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Basic information

Entry
Database: PDB / ID: 4xhg
TitleStructure of C. glabrata Hrr25 bound to ADP (formate condition)
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 / regulation of autophagosome assembly / pexophagy ...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 / regulation of autophagosome assembly / pexophagy / cellular bud neck / spindle pole body / preribosome, small subunit precursor / spindle assembly / ribosomal large subunit biogenesis / spindle microtubule / regulation of circadian rhythm / endocytosis / peroxisome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / ribosomal small subunit biogenesis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / DNA repair / protein serine/threonine kinase activity / Golgi apparatus / signal transduction / 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
ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)47,2243
Polymers46,7501
Non-polymers4732
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.460, 76.472, 84.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M sodium formate, 15% PEG 3350, and 5 mM TCEP. Cryoprotected with 20% glycerol.
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→44.6 Å / Num. obs: 25960 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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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: 2.15→44.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 1297 5 %
Rwork0.174 --
obs0.1761 25940 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 30 285 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073041
X-RAY DIFFRACTIONf_angle_d1.0434086
X-RAY DIFFRACTIONf_dihedral_angle_d14.2191153
X-RAY DIFFRACTIONf_chiral_restr0.042426
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1496-2.23570.27931490.22012689X-RAY DIFFRACTION100
2.2357-2.33740.24881360.2032726X-RAY DIFFRACTION100
2.3374-2.46070.21141550.18922688X-RAY DIFFRACTION100
2.4607-2.61480.22791260.17522722X-RAY DIFFRACTION100
2.6148-2.81670.23081430.16952740X-RAY DIFFRACTION100
2.8167-3.10010.20871400.17252741X-RAY DIFFRACTION100
3.1001-3.54850.1981520.162732X-RAY DIFFRACTION99
3.5485-4.47010.18771640.14622734X-RAY DIFFRACTION99
4.4701-44.61720.23121320.18872871X-RAY DIFFRACTION97
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)
10.03640.0207-0.01520.1087-0.00020.0465-0.08780.1107-0.0132-0.13720.07660.0895-0.1022-0.3173-00.14740.05490.0090.1780.01870.116613.3653-24.427910.407
20.36060.01510.02060.29210.0850.2096-0.01930.0580.03290.020.0234-0.0059-0.04020.007900.05650.0009-0.00450.04790.00880.057825.9624-24.9562-14.6917
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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