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- PDB-7vjp: Selenomethionine-derived Pectobacterium phage ZF40 apo-Aca2 -

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Basic information

Entry
Database: PDB / ID: 7vjp
TitleSelenomethionine-derived Pectobacterium phage ZF40 apo-Aca2
Componentsanti-CRISPR-associated protein Aca2
KeywordsTRANSCRIPTION / anti-crispr / Aca2 / anti-crispr-associated protein / crispr / repression
Function / homologyProtein of unknown function DUF1870 / Domain of unknown function (DUF1870) / YdiL domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / metal ion binding / DUF1870 family protein
Function and homology information
Biological speciesPectobacterium phage ZF40 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.594 Å
AuthorsLiu, Y.H. / Zhang, L.S. / Wu, B.X. / Huang, H.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.
Authors: Liu, Y. / Zhang, L. / Guo, M. / Chen, L. / Wu, B. / Huang, H.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 20, 2021ID: 7CQ9
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-CRISPR-associated protein Aca2
B: anti-CRISPR-associated protein Aca2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1664
Polymers27,9742
Non-polymers1922
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-42 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.650, 67.150, 42.600
Angle α, β, γ (deg.)90.000, 106.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein anti-CRISPR-associated protein Aca2


Mass: 13986.978 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium phage ZF40 (virus) / Gene: ZF40_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: H9C180
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Sodium Hepes pH 7.5, 2% PEG 400, 2.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→67.15 Å / Num. obs: 28345 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 8.8
Reflection shellResolution: 1.59→1.68 Å / Num. unique obs: 4100 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.594→32.96 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1365 4.82 %
Rwork0.152 26939 -
obs0.1536 28304 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.01 Å2 / Biso mean: 19.6162 Å2 / Biso min: 5.46 Å2
Refinement stepCycle: final / Resolution: 1.594→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 10 272 2171
Biso mean--33.94 31.55 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061952
X-RAY DIFFRACTIONf_angle_d0.7672646
X-RAY DIFFRACTIONf_chiral_restr0.041287
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d14.5681184
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.594-1.6510.22411480.18582670100
1.651-1.71710.19831490.1815265799
1.7171-1.79520.22411480.1782264798
1.7952-1.88990.20791140.1622272299
1.8899-2.00830.18031310.1649268899
2.0083-2.16330.20321480.1497265099
2.1633-2.38090.17431380.14252712100
2.3809-2.72530.18221350.1531270399
2.7253-3.4330.18391370.1467271399
3.433-32.960.17641170.1408277799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.94781.4306-4.29553.1489-1.5583.2230.2388-0.04340.23550.2448-0.0220.1569-0.5701-0.3701-0.24710.09730.01350.00420.1133-0.00430.0899-26.733848.352520.6467
24.1611-4.278-1.47997.5474-0.78284.86360.0953-0.46030.06490.318-0.0776-0.1488-0.1367-0.0018-0.01460.0991-0.0491-0.00410.158-0.00980.0725-24.907543.374729.7478
32.27590.14320.80532.6656-2.18872.1167-0.0218-0.1116-0.0842-0.07820.04530.17190.2381-0.0413-0.02840.1422-0.0429-0.01190.12950.01170.139-28.239936.106620.9643
43.265-0.5528-3.10932.5210.19783.01330.1903-0.2083-0.11070.27320.0739-0.12510.9565-0.2572-0.27050.2382-0.0529-0.05590.12720.0090.1351-29.371540.1228-0.868
52.4409-0.7861-0.48723.47923.56865.61860.20280.16820.0045-0.29420.0372-0.0332-0.2666-0.2737-0.13840.1284-0.0102-0.00410.10110.03650.1053-27.768451.3542-0.9717
63.789-0.4732-0.44380.8462-0.74651.70.39350.94950.6506-0.03730.04720.1286-0.3209-0.4121-0.17590.04140.12110.09380.38170.14880.235-36.412954.061310.2188
76.3587-1.2643-6.13991.22760.20369.47820.1092-0.08290.0881-0.06580.0797-0.00360.0470.0683-0.14870.07-0.0027-0.03020.06770.00270.0823-25.320348.37057.9678
82.8948-4.8243-1.45558.02152.47067.03090.06550.351-0.0107-0.3356-0.18710.06370.35080.09840.02770.1761-0.00680.02310.15180.00860.1405-21.685348.938-2.555
91.97650.40530.0454.02330.81162.5476-0.030.09810.1007-0.08820.0289-0.1734-0.11610.0430.01260.0401-0.00080.00470.07240.00710.0891-13.50158.65489.5069
103.9842-2.7145-0.2498.0226-0.42842.74220.0710.0750.4315-0.35290.0124-0.1999-0.28550.0204-0.05250.1479-0.00030.03270.10660.0020.1129-9.511656.00682.9872
116.1411-0.67953.65182.38982.72296.49140.19110.0256-0.3919-0.20620.0807-0.25270.5211-0.0531-0.14110.22010.0050.03750.1259-0.03940.1857-7.50431.19266.307
123.85461.23790.81193.3861-0.53152.91690.04840.0199-0.3702-0.042-0.0013-0.11890.2271-0.0216-0.04380.05570.02140.00510.06520.00140.0968-9.102339.692916.7345
134.35690.4467-0.24682.49330.21064.70570.0421-0.3014-0.46060.1043-0.0665-0.09120.41340.10590.05430.07260.0038-0.00630.10070.0270.1406-20.651136.71121.3767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 13 through 23 )B13 - 23
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 37 )B24 - 37
3X-RAY DIFFRACTION3chain 'B' and (resid 38 through 58 )B38 - 58
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 69 )B59 - 69
5X-RAY DIFFRACTION5chain 'B' and (resid 70 through 81 )B70 - 81
6X-RAY DIFFRACTION6chain 'B' and (resid 82 through 93 )B82 - 93
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 109 )B94 - 109
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 116 )B110 - 116
9X-RAY DIFFRACTION9chain 'A' and (resid -2 through 37 )A-2 - 37
10X-RAY DIFFRACTION10chain 'A' and (resid 38 through 58 )A38 - 58
11X-RAY DIFFRACTION11chain 'A' and (resid 59 through 74 )A59 - 74
12X-RAY DIFFRACTION12chain 'A' and (resid 75 through 116 )A75 - 116
13X-RAY DIFFRACTION13chain 'B' and (resid -2 through 12 )B-2 - 12

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