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- PDB-5yhr: Crystal structure of the anti-CRISPR protein, AcrF2 -

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Basic information

Entry
Database: PDB / ID: 5yhr
TitleCrystal structure of the anti-CRISPR protein, AcrF2
ComponentsAnti-CRISPR protein 30
KeywordsVIRAL PROTEIN / anti-CRISPR protein
Function / homologysymbiont-mediated suppression of host CRISPR-cas system / symbiont-mediated suppression of host adaptive immune response / virus-mediated perturbation of host defense response / Anti-CRISPR protein 30
Function and homology information
Biological speciesPseudomonas phage D3112 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
AuthorsHong, S. / Ka, D. / Bae, E.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: CRISPR RNA and anti-CRISPR protein binding to theXanthomonas albilineansCsy1-Csy2 heterodimer in the type I-F CRISPR-Cas system
Authors: Hong, S. / Ka, D. / Yoon, S.J. / Suh, N. / Jeong, M. / Suh, J.Y. / Bae, E.
History
DepositionSep 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-CRISPR protein 30
B: Anti-CRISPR protein 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6223
Polymers21,5822
Non-polymers401
Water5,441302
1
A: Anti-CRISPR protein 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8312
Polymers10,7911
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anti-CRISPR protein 30


Theoretical massNumber of molelcules
Total (without water)10,7911
Polymers10,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-22 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.546, 65.546, 101.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Anti-CRISPR protein 30 / Gene product 30 / gp30


Mass: 10791.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage D3112 (virus) / Gene: orf30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6TM72
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 51.85 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 21% (w/v) PEG 6000, 0.4 M CaCl2, 100 mM MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 50291 / % possible obs: 100 % / Redundancy: 27.9 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.02 / Rrim(I) all: 0.104 / Net I/σ(I): 29.79
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 25.6 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 6.43 / Num. unique obs: 4925 / Rpim(I) all: 0.117 / Rrim(I) all: 0.594 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data processing
PHENIXmodel building
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.34→23.174 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.13
RfactorNum. reflection% reflection
Rfree0.1962 1993 3.99 %
Rwork0.1796 --
obs0.1802 49975 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.34→23.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 1 303 1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061428
X-RAY DIFFRACTIONf_angle_d0.9611936
X-RAY DIFFRACTIONf_dihedral_angle_d13.444506
X-RAY DIFFRACTIONf_chiral_restr0.038218
X-RAY DIFFRACTIONf_plane_restr0.004256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3403-1.37390.19891380.16623300X-RAY DIFFRACTION98
1.3739-1.4110.19591390.15833331X-RAY DIFFRACTION99
1.411-1.45250.19131390.15163373X-RAY DIFFRACTION99
1.4525-1.49940.17821380.14933350X-RAY DIFFRACTION99
1.4994-1.5530.1541410.14093386X-RAY DIFFRACTION100
1.553-1.61510.15861410.1473392X-RAY DIFFRACTION100
1.6151-1.68860.20541430.14923418X-RAY DIFFRACTION100
1.6886-1.77760.19961410.16383404X-RAY DIFFRACTION100
1.7776-1.88890.19961430.17453418X-RAY DIFFRACTION100
1.8889-2.03470.18471410.17923426X-RAY DIFFRACTION100
2.0347-2.23930.18611440.17513464X-RAY DIFFRACTION100
2.2393-2.5630.21381440.18663479X-RAY DIFFRACTION100
2.563-3.22770.21061470.20223523X-RAY DIFFRACTION100
3.2277-23.17750.20081540.19933718X-RAY DIFFRACTION100

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