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- PDB-8jdi: Crystal structure of Cas7-AcrIF25 complex -

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Basic information

Entry
Database: PDB / ID: 8jdi
TitleCrystal structure of Cas7-AcrIF25 complex
Components
  • AcrIF25
  • CRISPR-associated protein Csy3
KeywordsDNA BINDING PROTEIN/INHIBITOR / DNA BINDING PROTEIN-inhibitor complex
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / defense response to virus / : / CRISPR-associated protein Csy3
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
Alcanivorax sp. KX64203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.372 Å
AuthorsYang, J. / Wang, J. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91940302 China
National Natural Science Foundation of China (NSFC)31725008 China
CitationJournal: To Be Published
Title: Crystal structure of Cas7-AcrIF25 complex
Authors: Yang, J. / Wang, J. / Wang, Y.
History
DepositionMay 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein Csy3
E: AcrIF25
C: CRISPR-associated protein Csy3
G: AcrIF25
B: CRISPR-associated protein Csy3
F: AcrIF25
D: CRISPR-associated protein Csy3
H: AcrIF25


Theoretical massNumber of molelcules
Total (without water)223,1358
Polymers223,1358
Non-polymers00
Water0
1
A: CRISPR-associated protein Csy3
E: AcrIF25
B: CRISPR-associated protein Csy3
F: AcrIF25


Theoretical massNumber of molelcules
Total (without water)111,5674
Polymers111,5674
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-33 kcal/mol
Surface area39510 Å2
MethodPISA
2
C: CRISPR-associated protein Csy3
G: AcrIF25
D: CRISPR-associated protein Csy3
H: AcrIF25


Theoretical massNumber of molelcules
Total (without water)111,5674
Polymers111,5674
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-29 kcal/mol
Surface area40260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.666, 119.008, 215.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 13 through 14 and (name N...
21(chain B and (resid 13 through 31 or (resid 32...
31(chain C and ((resid 13 through 14 and (name N...
41(chain D and ((resid 13 through 14 and (name N...
12(chain E and (resid 10 through 14 or (resid 15...
22(chain F and (resid 10 through 14 or (resid 15...
32(chain G and (resid 10 through 14 or (resid 15...
42(chain H and (resid 10 through 20 or (resid 21...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAPHEPHE(chain A and ((resid 13 through 14 and (name N...AA13 - 1413 - 14
121ILEILELYSLYS(chain A and ((resid 13 through 14 and (name N...AA5 - 3425 - 342
131ILEILELYSLYS(chain A and ((resid 13 through 14 and (name N...AA5 - 3425 - 342
141ILEILELYSLYS(chain A and ((resid 13 through 14 and (name N...AA5 - 3425 - 342
151ILEILELYSLYS(chain A and ((resid 13 through 14 and (name N...AA5 - 3425 - 342
211ALAALAALAALA(chain B and (resid 13 through 31 or (resid 32...BE13 - 3113 - 31
221GLNGLNGLNGLN(chain B and (resid 13 through 31 or (resid 32...BE3232
231ALAALAGLYGLY(chain B and (resid 13 through 31 or (resid 32...BE13 - 33313 - 333
241ALAALAGLYGLY(chain B and (resid 13 through 31 or (resid 32...BE13 - 33313 - 333
251ALAALAGLYGLY(chain B and (resid 13 through 31 or (resid 32...BE13 - 33313 - 333
261ALAALAGLYGLY(chain B and (resid 13 through 31 or (resid 32...BE13 - 33313 - 333
311ALAALAPHEPHE(chain C and ((resid 13 through 14 and (name N...CC13 - 1413 - 14
321ILEILELYSLYS(chain C and ((resid 13 through 14 and (name N...CC5 - 3425 - 342
331ILEILELYSLYS(chain C and ((resid 13 through 14 and (name N...CC5 - 3425 - 342
341ILEILELYSLYS(chain C and ((resid 13 through 14 and (name N...CC5 - 3425 - 342
411ALAALAPHEPHE(chain D and ((resid 13 through 14 and (name N...DG13 - 1413 - 14
421SERSERPHEPHE(chain D and ((resid 13 through 14 and (name N...DG10 - 33610 - 336
431SERSERPHEPHE(chain D and ((resid 13 through 14 and (name N...DG10 - 33610 - 336
441SERSERPHEPHE(chain D and ((resid 13 through 14 and (name N...DG10 - 33610 - 336
451SERSERPHEPHE(chain D and ((resid 13 through 14 and (name N...DG10 - 33610 - 336
112ALAALALEULEU(chain E and (resid 10 through 14 or (resid 15...EB10 - 1410 - 14
122ARGARGARGARG(chain E and (resid 10 through 14 or (resid 15...EB1515
132ASPASPGLYGLY(chain E and (resid 10 through 14 or (resid 15...EB9 - 1589 - 158
142ASPASPGLYGLY(chain E and (resid 10 through 14 or (resid 15...EB9 - 1589 - 158
152ASPASPGLYGLY(chain E and (resid 10 through 14 or (resid 15...EB9 - 1589 - 158
162ASPASPGLYGLY(chain E and (resid 10 through 14 or (resid 15...EB9 - 1589 - 158
212ALAALALEULEU(chain F and (resid 10 through 14 or (resid 15...FF10 - 1410 - 14
222ARGARGARGARG(chain F and (resid 10 through 14 or (resid 15...FF1515
232LYSLYSGLYGLY(chain F and (resid 10 through 14 or (resid 15...FF7 - 1587 - 158
242LYSLYSGLYGLY(chain F and (resid 10 through 14 or (resid 15...FF7 - 1587 - 158
252LYSLYSGLYGLY(chain F and (resid 10 through 14 or (resid 15...FF7 - 1587 - 158
262LYSLYSGLYGLY(chain F and (resid 10 through 14 or (resid 15...FF7 - 1587 - 158
312ALAALALEULEU(chain G and (resid 10 through 14 or (resid 15...GD10 - 1410 - 14
322ARGARGARGARG(chain G and (resid 10 through 14 or (resid 15...GD1515
332PROPROGLYGLY(chain G and (resid 10 through 14 or (resid 15...GD8 - 1598 - 159
342PROPROGLYGLY(chain G and (resid 10 through 14 or (resid 15...GD8 - 1598 - 159
352PROPROGLYGLY(chain G and (resid 10 through 14 or (resid 15...GD8 - 1598 - 159
362PROPROGLYGLY(chain G and (resid 10 through 14 or (resid 15...GD8 - 1598 - 159
412ALAALAVALVAL(chain H and (resid 10 through 20 or (resid 21...HH10 - 2010 - 20
422LYSLYSLYSLYS(chain H and (resid 10 through 20 or (resid 21...HH2121
432PROPROGLYGLY(chain H and (resid 10 through 20 or (resid 21...HH8 - 1588 - 158
442PROPROGLYGLY(chain H and (resid 10 through 20 or (resid 21...HH8 - 1588 - 158
452PROPROGLYGLY(chain H and (resid 10 through 20 or (resid 21...HH8 - 1588 - 158
462PROPROGLYGLY(chain H and (resid 10 through 20 or (resid 21...HH8 - 1588 - 158

NCS ensembles :
ID
1
2

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Components

#1: Protein
CRISPR-associated protein Csy3


Mass: 37579.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: UCBPP-PA14 / Gene: csy3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02MM1
#2: Protein
AcrIF25


Mass: 18204.455 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax sp. KX64203 (bacteria) / Gene: A3Q32_18550 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A154C2D0

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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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane, pH 6.5, 21 % PEG3350, 0.2 M Lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.37→50 Å / Num. obs: 40193 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.981 / Net I/σ(I): 8.4
Reflection shellResolution: 3.4→3.48 Å / Num. unique obs: 2587 / CC1/2: 0.372

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B45, 7WXV

6b45

7wxv
PDB Unreleased entry


Resolution: 3.372→49.426 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1752 4.88 %
Rwork0.2179 34174 -
obs0.2193 35926 89.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.44 Å2 / Biso mean: 53.924 Å2 / Biso min: 13.46 Å2
Refinement stepCycle: final / Resolution: 3.372→49.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13481 0 0 0 13481
Num. residues----1808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4732X-RAY DIFFRACTION18.411TORSIONAL
12B4732X-RAY DIFFRACTION18.411TORSIONAL
13C4732X-RAY DIFFRACTION18.411TORSIONAL
14D4732X-RAY DIFFRACTION18.411TORSIONAL
21E2530X-RAY DIFFRACTION18.411TORSIONAL
22F2530X-RAY DIFFRACTION18.411TORSIONAL
23G2530X-RAY DIFFRACTION18.411TORSIONAL
24H2530X-RAY DIFFRACTION18.411TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.372-3.46290.3042530.386730
3.4629-3.56470.3169860.279166957
3.5647-3.67970.2661090.26238482
3.6797-3.81120.30121470.262274595
3.8112-3.96370.26421470.2422287398
3.9637-4.14410.27321460.22892907100
4.1441-4.36240.25831280.21442929100
4.3624-4.63560.21271710.18992896100
4.6356-4.99320.23471530.19142925100
4.9932-5.4950.20471490.22957100
5.495-6.28880.27871450.21652963100
6.2888-7.9180.23851520.20723003100
7.918-49.40.20991660.1828305698

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