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- PDB-5b7i: Cas3-AcrF3 complex -

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Basic information

Entry
Database: PDB / ID: 5b7i
TitleCas3-AcrF3 complex
Components
  • CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
  • Uncharacterized protein AcrF3
KeywordsHYDROLASE/UNKNOWN FUNCTION / DNA nuclease / phagy protein / Anti-CRISPR / HYDROLASE-UNKNOWN FUNCTION complex
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily ...: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / HD Cas3-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phage protein / CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas phage JBD5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWang, X. / Zhu, Y.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China81322024 China
National Natural Science Foundation of China81561130162 China
National Natural Science Foundation of China31370722 China
National Natural Science Foundation of China81530068 China
National Natural Science Foundation of China81501717 China
Natural Science Foundation of Zhejiang province, ChinaLR13C05001 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structural basis of Cas3 inhibition by the bacteriophage protein AcrF3
Authors: Wang, X. / Yao, D. / Xu, J.G. / Li, A.R. / Xu, J. / Fu, P. / Zhou, Y. / Zhu, Y.
History
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
B: Uncharacterized protein AcrF3
C: Uncharacterized protein AcrF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,2876
Polymers157,7803
Non-polymers5073
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-36 kcal/mol
Surface area48850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.304, 127.197, 218.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST


Mass: 122554.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: cas3, PA14_33340 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
References: UniProt: Q02ML8, Hydrolases; Acting on ester bonds, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Uncharacterized protein AcrF3


Mass: 17612.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: L7P7R7
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 529 IS GLY ACCORDING TO AUTHOR SEQUENCING RESULTS.

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350, 100mM ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.6→109.23 Å / Num. obs: 41828 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.117 / Net I/av σ(I): 25.067 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.6912.50.8161100
2.69-2.813.40.621100
2.8-2.9313.20.4511100
2.93-3.0812.50.3131100
3.08-3.2813.30.2151100
3.28-3.5313.30.1471100
3.53-3.8812.50.1071100
3.88-4.4513.50.0771100
4.45-5.6130.0641100
5.6-5012.70.0561100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.988 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.341
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 2105 5 %RANDOM
Rwork0.2038 ---
obs0.2061 39622 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.54 Å2 / Biso mean: 42.344 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.18 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10454 0 29 85 10568
Biso mean--67.79 31.12 -
Num. residues----1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910729
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.95214547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54751314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43522.404545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.36615129
X-RAY DIFFRACTIONr_chiral_restr0.0870.21549
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218363
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 140 -
Rwork0.266 2614 -
all-2754 -
obs--95 %

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