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- PDB-4zgp: Structure of Cdc123 from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 4zgp
TitleStructure of Cdc123 from Schizosaccharomyces pombe
ComponentsCell division cycle protein 123
KeywordsCELL CYCLE / ATP-grap fold / eIF2
Function / homology
Function and homology information


eukaryotic translation initiation factor 2 complex assembly / protein folding chaperone / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Cell division cycle protein 123 / D123
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Translation initiation factor eIF2 assembly protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3583
Polymers67,9312
Non-polymers4271
Water5,963331
1
A: Cell division cycle protein 123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3932
Polymers33,9661
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division cycle protein 123


Theoretical massNumber of molelcules
Total (without water)33,9661
Polymers33,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.483, 91.436, 86.006
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21B-371-

HOH

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Components

#1: Protein Cell division cycle protein 123 / cdc123


Mass: 33965.578 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9P7N5
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 297 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: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→43.2 Å / Num. all: 56281 / Num. obs: 56189 / % possible obs: 98.1 % / Redundancy: 3 % / Rsym value: 0.033 / Net I/σ(I): 19
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGO

4zgo


Resolution: 1.85→43.2 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2869 5.1 %
Rwork0.1883 --
obs0.1899 56273 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 27 331 4459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084292
X-RAY DIFFRACTIONf_angle_d1.0955835
X-RAY DIFFRACTIONf_dihedral_angle_d14.2591601
X-RAY DIFFRACTIONf_chiral_restr0.046645
X-RAY DIFFRACTIONf_plane_restr0.006723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8479-1.87980.37121330.31952524X-RAY DIFFRACTION94
1.8798-1.9140.31851430.2882683X-RAY DIFFRACTION98
1.914-1.95080.27011500.26222592X-RAY DIFFRACTION97
1.9508-1.99060.30761540.23992670X-RAY DIFFRACTION98
1.9906-2.03390.26761390.23362661X-RAY DIFFRACTION99
2.0339-2.08120.27441450.23182669X-RAY DIFFRACTION98
2.0812-2.13330.25331450.222639X-RAY DIFFRACTION98
2.1333-2.19090.26411510.21142694X-RAY DIFFRACTION99
2.1909-2.25540.24511540.20492648X-RAY DIFFRACTION98
2.2554-2.32820.24231370.20862702X-RAY DIFFRACTION99
2.3282-2.41140.2481530.21032669X-RAY DIFFRACTION99
2.4114-2.50790.28341390.20842678X-RAY DIFFRACTION99
2.5079-2.62210.23011380.20442699X-RAY DIFFRACTION99
2.6221-2.76030.25521340.2072678X-RAY DIFFRACTION99
2.7603-2.93320.23921560.20752678X-RAY DIFFRACTION99
2.9332-3.15960.2431410.20072696X-RAY DIFFRACTION99
3.1596-3.47740.20951150.18692716X-RAY DIFFRACTION98
3.4774-3.98030.18641400.15972689X-RAY DIFFRACTION98
3.9803-5.01360.17611560.14532684X-RAY DIFFRACTION99
5.0136-43.24330.18431460.16712735X-RAY DIFFRACTION98

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