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- PDB-7f7p: AcrIIC4 -

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Basic information

Entry
Database: PDB / ID: 7f7p
TitleAcrIIC4
Componentsanti-CRISPR protein AcrIIC4
KeywordsIMMUNE SYSTEM / Anti-CRISPR AcrIIC4 / Inhibitor of CRISPR-Cas 9
Function / homologyUncharacterized protein
Function and homology information
Biological speciesHaemophilus parainfluenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.03 Å
AuthorsKim, G.E. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2021
Title: Crystal structure of the anti-CRISPR, AcrIIC4.
Authors: Kim, G.E. / Lee, S.Y. / Park, H.H.
History
DepositionJun 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-CRISPR protein AcrIIC4
B: anti-CRISPR protein AcrIIC4


Theoretical massNumber of molelcules
Total (without water)22,1132
Polymers22,1132
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.790, 52.110, 54.390
Angle α, β, γ (deg.)90.00, 95.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein anti-CRISPR protein AcrIIC4


Mass: 11056.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parainfluenzae (bacteria) / Gene: NCTC10672_00033, NCTC10672_02354 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A377JKY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M CHES/Sodium hydroxide pH 9.5 30 % w/v PEG 3000

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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: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→29.26 Å / Num. obs: 11895 / % possible obs: 99.84 % / Redundancy: 6.8 % / Rrim(I) all: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 2.03→2.103 Å / Num. unique obs: 1183 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
MxDCdata collection
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.03→29.26 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 595 5 %
Rwork0.2259 --
obs0.2285 11893 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 0 33 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071528
X-RAY DIFFRACTIONf_angle_d0.9412044
X-RAY DIFFRACTIONf_dihedral_angle_d13.91190
X-RAY DIFFRACTIONf_chiral_restr0.049220
X-RAY DIFFRACTIONf_plane_restr0.005266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.230.22881470.19082805X-RAY DIFFRACTION100
2.23-2.560.29831480.23912800X-RAY DIFFRACTION100
2.56-3.220.33631480.28222825X-RAY DIFFRACTION100
3.22-29.260.25781520.20582868X-RAY DIFFRACTION100

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