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- PDB-5yet: Structure of R354_WT -

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Basic information

Entry
Database: PDB / ID: 5yet
TitleStructure of R354_WT
ComponentsUncharacterized protein R354
KeywordsNUCLEAR PROTEIN / MIMIVIRE / Cas4-like / nuclease / R354
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 / SAD / Resolution: 2.806 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 1.0Jun 20, 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 / 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: Uncharacterized protein R354
B: Uncharacterized protein R354


Theoretical massNumber of molelcules
Total (without water)94,4692
Polymers94,4692
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-15 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.846, 57.809, 99.948
Angle α, β, γ (deg.)90.00, 108.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein R354


Mass: 47234.547 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 139-537
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R354 / Production host: Escherichia coli DH1 (bacteria) / Strain (production host): DH1 / References: UniProt: Q5UQV1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM ammonium tartrate, 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: 2.806→48.949 Å / Num. obs: 22531 / % possible obs: 85.48 % / Redundancy: 4.8 % / Net I/σ(I): 13.05

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
PHENIXdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.806→48.949 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2416 1059 4.7 %
Rwork0.1945 --
obs0.1967 22530 85.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.806→48.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 0 49 6666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026776
X-RAY DIFFRACTIONf_angle_d0.4959137
X-RAY DIFFRACTIONf_dihedral_angle_d12.0554101
X-RAY DIFFRACTIONf_chiral_restr0.041959
X-RAY DIFFRACTIONf_plane_restr0.0031170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8057-2.93340.316820.27131570X-RAY DIFFRACTION51
2.9334-3.0880.33321200.26532261X-RAY DIFFRACTION73
3.088-3.28150.27431550.24422527X-RAY DIFFRACTION82
3.2815-3.53480.31731220.2352751X-RAY DIFFRACTION88
3.5348-3.89040.25391410.19652922X-RAY DIFFRACTION93
3.8904-4.4530.19951410.16963112X-RAY DIFFRACTION98
4.453-5.6090.21371440.16053105X-RAY DIFFRACTION99
5.609-48.95660.19051540.16943223X-RAY DIFFRACTION99

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