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- PDB-5gnf: Crystal structure of anti-CRISPR protein AcrF3 -

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Basic information

Entry
Database: PDB / ID: 5gnf
TitleCrystal structure of anti-CRISPR protein AcrF3
ComponentsUncharacterized protein AcrF3
KeywordsUNKNOWN FUNCTION / anti-CRISPR / phage
Function / homology: / Cas3 inhibitor AcrF3 / metal ion binding / Phage protein
Function and homology information
Biological speciesPseudomonas phage JBD5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWang, J. / Wang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China91440201 China
Ministry of Science and Technology (China)2014CB910102 China
Chinese Academy of SciencesXDB08010203 China
CitationJournal: Cell Res / Year: 2016
Title: A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses.
Authors: Jiuyu Wang / Jun Ma / Zhi Cheng / Xu Meng / Lilan You / Min Wang / Xinzheng Zhang / Yanli Wang /
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein AcrF3
B: Uncharacterized protein AcrF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9075
Polymers31,7872
Non-polymers1203
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-26 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.944, 84.944, 63.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Uncharacterized protein AcrF3


Mass: 15893.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Gene: JBD5_035 / Production host: Escherichia coli (E. coli) / References: UniProt: L7P7R7
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.1 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% (w/v) PEG 8000, 100mM MES, 200mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 41528 / % possible obs: 99.9 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 43.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→42.472 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 1992 4.8 %
Rwork0.17 --
obs0.1711 41497 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 3 319 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062230
X-RAY DIFFRACTIONf_angle_d0.7813024
X-RAY DIFFRACTIONf_dihedral_angle_d16.7381304
X-RAY DIFFRACTIONf_chiral_restr0.047321
X-RAY DIFFRACTIONf_plane_restr0.004394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.53780.29741460.26692814X-RAY DIFFRACTION99
1.5378-1.57930.22271380.23292799X-RAY DIFFRACTION100
1.5793-1.62580.22121400.20832787X-RAY DIFFRACTION100
1.6258-1.67830.22251410.19082823X-RAY DIFFRACTION100
1.6783-1.73830.19741420.17912805X-RAY DIFFRACTION100
1.7383-1.80790.19651430.17592806X-RAY DIFFRACTION100
1.8079-1.89020.23171440.17992825X-RAY DIFFRACTION100
1.8902-1.98980.19211400.16152810X-RAY DIFFRACTION100
1.9898-2.11450.21041370.16252826X-RAY DIFFRACTION100
2.1145-2.27770.17131420.1652799X-RAY DIFFRACTION100
2.2777-2.50690.19761450.16752846X-RAY DIFFRACTION100
2.5069-2.86960.22961450.17982829X-RAY DIFFRACTION100
2.8696-3.61510.17541430.16512835X-RAY DIFFRACTION100
3.6151-42.4890.16351460.15352901X-RAY DIFFRACTION100

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