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- PDB-7chr: AcrIF9 -

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Basic information

Entry
Database: PDB / ID: 7chr
TitleAcrIF9
Componentsanti-CRISPR AcrIF9
KeywordsRNA BINDING PROTEIN / anti-CRISPR AcrIF9
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPhotobacterium damselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.21 Å
AuthorsKim, G.E. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Febs Open Bio / Year: 2020
Title: A high-resolution (1.2 angstrom ) crystal structure of the anti-CRISPR protein AcrIF9.
Authors: Kim, G.E. / Lee, S.Y. / Park, H.H.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: anti-CRISPR AcrIF9


Theoretical massNumber of molelcules
Total (without water)8,8851
Polymers8,8851
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Multi angle light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.230, 31.350, 80.700
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 anti-CRISPR AcrIF9


Mass: 8885.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium damselae (bacteria) / Gene: BST98_20680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S2CJ39
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.96 Å3/Da / Density % sol: 37.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.06
Details: 0.1 M Tris-HCl pH 8.5 0.18 M Ammonium acetate 25 %(w/v) PEG 3350 40 %(v/v) 2,2,2-Trifluoroethanol

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→29.24 Å / Num. obs: 271001 / % possible obs: 99.97 % / Redundancy: 12.4 % / Rrim(I) all: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 1.24→1.27 Å / Num. unique obs: 21825 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MxDCdata collection
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.21→29.222 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 1092 5.01 %
Rwork0.1882 --
obs0.1885 21812 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→29.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms623 0 0 104 727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005677
X-RAY DIFFRACTIONf_angle_d0.799919
X-RAY DIFFRACTIONf_dihedral_angle_d2.364545
X-RAY DIFFRACTIONf_chiral_restr0.08397
X-RAY DIFFRACTIONf_plane_restr0.004121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.26510.49881340.41112539X-RAY DIFFRACTION100
1.2651-1.33180.3111330.30282530X-RAY DIFFRACTION100
1.3318-1.41520.25551340.23962542X-RAY DIFFRACTION100
1.4152-1.52450.23721360.20792565X-RAY DIFFRACTION100
1.5245-1.67790.18681350.17092574X-RAY DIFFRACTION100
1.6779-1.92060.20511360.1712587X-RAY DIFFRACTION100
1.9206-2.41960.17721380.1692626X-RAY DIFFRACTION100
2.4196-2.50.16951460.1522757X-RAY DIFFRACTION100

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