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- PDB-4zgo: Structure of C-terminally truncated Cdc123 from Schizosaccharomyc... -

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Basic information

Entry
Database: PDB / ID: 4zgo
TitleStructure of C-terminally truncated Cdc123 from Schizosaccharomyces pombe
ComponentsCell division cycle protein 123
KeywordsCELL CYCLE / ATP-grap fold / eIF2 assembly
Function / homologyeukaryotic translation initiation factor 2 complex assembly / Cell division cycle protein 123 / D123 / protein folding chaperone / magnesium ion binding / ATP binding / cytosol / cytoplasm / Translation initiation factor eIF2 assembly protein
Function and homology information
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.063 Å
AuthorsPanvert, M. / Dubiez, E. / Arnold, L. / Perez, J. / Seufert, W. / Mechulam, Y. / Schmitt, E.
Funding support France, 2items
OrganizationGrant numberCountry
CNRSUMR7654 France
Ecole polytechniqueUMR7654 France
CitationJournal: Structure / Year: 2015
Title: Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.
Authors: Panvert, M. / Dubiez, E. / Arnold, L. / Perez, J. / Mechulam, Y. / Seufert, W. / Schmitt, E.
History
DepositionApr 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: Cell division cycle protein 123
B: Cell division cycle protein 123


Theoretical massNumber of molelcules
Total (without water)78,2202
Polymers78,2202
Non-polymers00
Water3,567198
1
A: Cell division cycle protein 123


Theoretical massNumber of molelcules
Total (without water)39,1101
Polymers39,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division cycle protein 123


Theoretical massNumber of molelcules
Total (without water)39,1101
Polymers39,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.600, 91.710, 86.240
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division cycle protein 123


Mass: 39110.246 Da / Num. of mol.: 2 / Fragment: unp residues 21-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cdc123, SPAP27G11.03 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P7N5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 12% PEG3350, 4% tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→45.8 Å / Num. all: 41180 / Num. obs: 41180 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 2.06→2.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low-resolution model from SAD experiments

Resolution: 2.063→45.8 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 2040 5.03 %
Rwork0.1934 --
obs0.1952 40569 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.063→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 0 198 4333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084248
X-RAY DIFFRACTIONf_angle_d1.0935760
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851564
X-RAY DIFFRACTIONf_chiral_restr0.044635
X-RAY DIFFRACTIONf_plane_restr0.006720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0625-2.11050.34771170.32262195X-RAY DIFFRACTION86
2.1105-2.16330.34541450.29642609X-RAY DIFFRACTION100
2.1633-2.22180.34141510.27622552X-RAY DIFFRACTION100
2.2218-2.28710.32521350.26152575X-RAY DIFFRACTION100
2.2871-2.3610.34431410.25062567X-RAY DIFFRACTION100
2.361-2.44530.27771370.2542590X-RAY DIFFRACTION100
2.4453-2.54320.35131320.25522593X-RAY DIFFRACTION100
2.5432-2.6590.26271320.2442588X-RAY DIFFRACTION100
2.659-2.79910.28171230.23962600X-RAY DIFFRACTION100
2.7991-2.97450.27951650.24042594X-RAY DIFFRACTION100
2.9745-3.20410.29051270.22862583X-RAY DIFFRACTION100
3.2041-3.52640.2641100.20912630X-RAY DIFFRACTION100
3.5264-4.03640.2151400.17782599X-RAY DIFFRACTION100
4.0364-5.08440.19191430.15232603X-RAY DIFFRACTION100
5.0844-45.86630.15111420.14932651X-RAY DIFFRACTION100

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