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Basic information

Entry
Database: PDB / ID: 5yeu
TitleStructural and mechanistic analyses reveal a unique Cas4-like protein in the mimivirus virophage resistance element system
ComponentsUncharacterized protein R354
KeywordsNUCLEAR PROTEIN / MIMIVIRE / Cas4-like / Nuclease / RIBOSOMAL PROTEIN
Function / homologyPutative phage-type endonuclease / YqaJ viral recombinase / YqaJ-like viral recombinase domain / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / Uncharacterized protein R354
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.001 Å
AuthorsDou, C. / Yu, M.J. / Gu, Y.J. / Cheng, W.
CitationJournal: Iscience / Year: 2018
Title: Structural and Mechanistic Analyses Reveal a Unique Cas4-like Protein in the Mimivirus Virophage Resistance Element System.
Authors: Dou, C. / Yu, M. / Gu, Y. / Wang, J. / Yin, K. / Nie, C. / Zhu, X. / Qi, S. / Wei, Y. / Cheng, W.
History
DepositionSep 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein R354
B: Uncharacterized protein R354
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0816
Polymers91,9842
Non-polymers974
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-38 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.259, 93.453, 123.190
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 Uncharacterized protein R354


Mass: 45991.996 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 141-531 / Mutation: E408A, K409A, M416A, R431A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R354
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpT4 (others)
References: UniProt: Q5UQV1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM magnesium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.001→40.252 Å / Num. obs: 18840 / % possible obs: 99.71 % / Redundancy: 12.6 % / Net I/σ(I): 10.339
Reflection shellResolution: 3.001→3.1592 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHENIXdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.001→40.252 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 916 4.86 %
Rwork0.2236 --
obs0.2255 18840 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→40.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 4 23 6336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026457
X-RAY DIFFRACTIONf_angle_d0.5958715
X-RAY DIFFRACTIONf_dihedral_angle_d13.0153899
X-RAY DIFFRACTIONf_chiral_restr0.042922
X-RAY DIFFRACTIONf_plane_restr0.0041116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.15920.33311270.2952511X-RAY DIFFRACTION99
3.1592-3.3570.3141560.27092478X-RAY DIFFRACTION100
3.357-3.61610.33131380.25032538X-RAY DIFFRACTION100
3.6161-3.97970.23841020.23152568X-RAY DIFFRACTION100
3.9797-4.55480.24821380.19552545X-RAY DIFFRACTION100
4.5548-5.7360.20111200.19262599X-RAY DIFFRACTION100
5.736-40.25580.26051350.2152685X-RAY DIFFRACTION99

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