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- PDB-8jdh: Crystal structure of anti-CRISPR AcrIF25 -

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Basic information

Entry
Database: PDB / ID: 8jdh
TitleCrystal structure of anti-CRISPR AcrIF25
ComponentsAcrIF25
KeywordsDNA BINDING PROTEIN / inhibitor
Function / homology:
Function and homology information
Biological speciesAlcanivorax sp. KX64203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 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: Nature / Year: 2024
Title: An anti-CRISPR that pulls apart a CRISPR-Cas complex.
Authors: Trost, C.N. / Yang, J. / Garcia, B. / Hidalgo-Reyes, Y. / Fung, B.C.M. / Wang, J. / Lu, W.T. / Maxwell, K.L. / Wang, Y. / Davidson, A.R.
History
DepositionMay 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Sep 4, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIF25
B: AcrIF25


Theoretical massNumber of molelcules
Total (without water)36,7842
Polymers36,7842
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-18 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.953, 52.289, 85.121
Angle α, β, γ (deg.)90.000, 105.910, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...
21(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...AA99
12ASPASPGLYGLY(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...AA9 - 1589 - 158
13ASPASPGLYGLY(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...AA9 - 1589 - 158
14ASPASPGLYGLY(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...AA9 - 1589 - 158
15ASPASPGLYGLY(CHAIN A AND ((RESID 9 THROUGH 11 AND (NAME N...AA9 - 1589 - 158
21ASPASPASPASP(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB99
22VALVALVALVAL(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB1616
23VALVALVALVAL(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB2020
24ASPASPALAALA(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB9 - 1609 - 160
25LEULEULEULEU(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB1111
26VALVALVALVAL(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB134134
27ALAALAALAALA(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB136136
28MSEMSEMSEMSE(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB139139
29GLNGLNGLNGLN(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB155155
210ASPASPALAALA(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB9 - 1609 - 160
211ASPASPALAALA(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB9 - 1609 - 160
212ASPASPALAALA(CHAIN B AND (RESID 9 THROUGH 14 OR RESID 16...BB9 - 1609 - 160

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Components

#1: Protein AcrIF25


Mass: 18392.035 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M SODIUM ACETATE, PH 5.0, 11 % MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 35124 / % possible obs: 98.7 % / Redundancy: 13.1 % / CC1/2: 0.996 / Net I/σ(I): 27.3
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 1605 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→44.19 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1713 5.08 %
Rwork0.168 31989 -
obs0.169 33702 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.79 Å2 / Biso mean: 26.23 Å2 / Biso min: 7.16 Å2
Refinement stepCycle: final / Resolution: 1.77→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 278 2503
Biso mean---35.69 -
Num. residues----295
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A746X-RAY DIFFRACTIONPOSITIONAL0
12B746X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.82190.2361130.22051933204669
1.8219-1.88070.23031020.19352259236180
1.8807-1.94790.24431240.19442571269591
1.9479-2.02590.21181370.19022772290998
2.0259-2.11810.18331470.17272768291599
2.1181-2.22970.2491580.173927712929100
2.2297-2.36940.20371430.167728242967100
2.3694-2.55230.19641690.16782772294199
2.5523-2.80920.19821600.166328232983100
2.8092-3.21560.18771680.17272767293599
3.2156-4.05080.1621430.148128422985100
4.0508-44.190.17091490.16282887303699
Refinement TLS params.Method: refined / Origin x: 33.0499 Å / Origin y: 29.5417 Å / Origin z: 14.7799 Å
111213212223313233
T0.1051 Å2-0.0008 Å2-0.0051 Å2-0.1067 Å2-0.0093 Å2--0.0748 Å2
L1.1371 °20.1281 °2-0.1759 °2-0.2249 °2-0.1247 °2--0.2114 °2
S0.0111 Å °-0.1881 Å °0.0195 Å °0.0355 Å °0.0025 Å °-0.0103 Å °-0.0103 Å °-0.0019 Å °0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA9 - 158
2X-RAY DIFFRACTION1ALLA201 - 345
3X-RAY DIFFRACTION1ALLB9 - 160
4X-RAY DIFFRACTION1ALLB201 - 334

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