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- PDB-4xah: X-ray crystal structure of S. cerevisiae Cgi121 -

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Basic information

Entry
Database: PDB / ID: 4xah
TitleX-ray crystal structure of S. cerevisiae Cgi121
ComponentsEKC/KEOPS complex subunit CGI121
KeywordsPROTEIN BINDING / KEOPS / Cgi121 / Bud32-binding protein
Function / homology
Function and homology information


EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / tRNA binding / chromosome, telomeric region / positive regulation of transcription by RNA polymerase II / nucleoplasm ...EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / tRNA binding / chromosome, telomeric region / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
PF0523-like / CGI121/TPRKB / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EKC/KEOPS complex subunit CGI121
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsZhang, W. / Graille, M. / Collinet, B. / van Tilbeurgh, H.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex.
Authors: Zhang, W. / Collinet, B. / Graille, M. / Daugeron, M.C. / Lazar, N. / Libri, D. / Durand, D. / van Tilbeurgh, H.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: EKC/KEOPS complex subunit CGI121
B: EKC/KEOPS complex subunit CGI121


Theoretical massNumber of molelcules
Total (without water)43,1842
Polymers43,1842
Non-polymers00
Water6,900383
1
A: EKC/KEOPS complex subunit CGI121


Theoretical massNumber of molelcules
Total (without water)21,5921
Polymers21,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EKC/KEOPS complex subunit CGI121


Theoretical massNumber of molelcules
Total (without water)21,5921
Polymers21,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.650, 76.900, 84.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EKC/KEOPS complex subunit CGI121 / CGI-121 homolog


Mass: 21591.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CGI121, YML036W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q03705
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10 mM Tris-HCl pH 7.5, 100mM NaCl, 10mM 2-mercaptoethanol,0.6 M sodium citrate, 0.05 M sodium citrate pH 5.0
PH range: 5.0 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 115741 / Num. obs: 32377 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.5 % / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Cootmodel building
SHELXDEphasing
PHENIX(phenix.refine)refinement
RefinementResolution: 2.5→20 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1944 5.03 %
Rwork0.1852 --
obs0.1878 38679 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.763 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9791 Å20 Å2-0 Å2
2--3.2108 Å20 Å2
3----5.1899 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 0 383 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072958
X-RAY DIFFRACTIONf_angle_d0.9993993
X-RAY DIFFRACTIONf_dihedral_angle_d16.861153
X-RAY DIFFRACTIONf_chiral_restr0.068462
X-RAY DIFFRACTIONf_plane_restr0.008512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.39371290.31132628X-RAY DIFFRACTION99
1.9476-2.00020.34251250.25492649X-RAY DIFFRACTION100
2.0002-2.05910.30661520.22952612X-RAY DIFFRACTION100
2.0591-2.12550.2491320.21292664X-RAY DIFFRACTION100
2.1255-2.20150.23311600.21172624X-RAY DIFFRACTION99
2.2015-2.28960.29171430.21392631X-RAY DIFFRACTION99
2.2896-2.39380.24911460.19612624X-RAY DIFFRACTION100
2.3938-2.51990.24541280.19172662X-RAY DIFFRACTION99
2.5199-2.67780.2091340.18042650X-RAY DIFFRACTION99
2.6778-2.88440.2231310.18472675X-RAY DIFFRACTION99
2.8844-3.17450.24811350.18132662X-RAY DIFFRACTION98
3.1745-3.63340.22961550.17872642X-RAY DIFFRACTION98
3.6334-4.57610.19211460.13792607X-RAY DIFFRACTION96
4.5761-34.53440.20191280.15992405X-RAY DIFFRACTION84

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