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- PDB-4xh0: Structure of C. glabrata Hrr25 bound to ADP (SO4 condition) -

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Basic information

Entry
Database: PDB / ID: 4xh0
TitleStructure of C. glabrata Hrr25 bound to ADP (SO4 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 / cellular bud tip / tRNA wobble uridine modification / 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 / cellular bud tip / tRNA wobble uridine modification / 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 / ribosomal small subunit biogenesis / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 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 4, 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 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)47,7548
Polymers46,7501
Non-polymers1,0047
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.788, 76.974, 84.277
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, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, 19% PEG 3350, and 5 mM TCEP
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→71.8 Å / Num. obs: 31839 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.9
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→52.499 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 1606 5.05 %
Rwork0.1659 --
obs0.1676 31824 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→52.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 57 293 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123016
X-RAY DIFFRACTIONf_angle_d1.254058
X-RAY DIFFRACTIONf_dihedral_angle_d13.7341137
X-RAY DIFFRACTIONf_chiral_restr0.056421
X-RAY DIFFRACTIONf_plane_restr0.006505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9894-2.05360.30231590.27192702X-RAY DIFFRACTION98
2.0536-2.1270.26251400.23392722X-RAY DIFFRACTION98
2.127-2.21220.26821580.19592765X-RAY DIFFRACTION99
2.2122-2.31290.22461390.17712734X-RAY DIFFRACTION98
2.3129-2.43480.18661510.16922751X-RAY DIFFRACTION99
2.4348-2.58740.21881370.16072750X-RAY DIFFRACTION98
2.5874-2.78710.20271400.15782772X-RAY DIFFRACTION98
2.7871-3.06760.20091360.16472758X-RAY DIFFRACTION98
3.0676-3.51140.20221530.15562747X-RAY DIFFRACTION96
3.5114-4.42370.13781630.1312722X-RAY DIFFRACTION96
4.4237-52.51780.20111300.16222795X-RAY DIFFRACTION92
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)
12.3509-0.1414-0.11192.0321-0.3531.3307-0.0667-0.18210.31220.25220.22360.4261-0.2132-0.5726-0.11580.23130.07070.03860.36830.03030.232513.4427-24.774211.1813
21.43880.04380.14031.24030.26781.0241-0.02640.14160.2134-0.07520.0134-0.0512-0.15950.00970.01370.11370.0055-0.0050.16380.01570.112825.521-25.398-14.3258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 397 )

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