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- PDB-7fa3: Selenomethionine-derived structure of Aca1 in Pseudomonas phage JBD30 -

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Basic information

Entry
Database: PDB / ID: 7fa3
TitleSelenomethionine-derived structure of Aca1 in Pseudomonas phage JBD30
ComponentsAca1
KeywordsTRANSCRIPTION / CRISPR / anti-CRISPR / anti-CRISPR-associated / DNA binding / autoregulation
Function / homologyLambda repressor-like, DNA-binding domain superfamily / DNA binding / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.847 Å
AuthorsLiu, Y. / Zhang, L. / Wu, B. / Huang, H.
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
DepositionJul 5, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 21, 2021ID: 7C0B
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aca1
B: Aca1


Theoretical massNumber of molelcules
Total (without water)18,8272
Polymers18,8272
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-16 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.429, 50.443, 64.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11THRTHRGLNGLN(chain A and (resseq 8:32 or resseq 34:43 or (resid...AA8 - 3213 - 37
12ARGARGVALVAL(chain A and (resseq 8:32 or resseq 34:43 or (resid...AA34 - 4539 - 50
13TYRTYRASPASP(chain A and (resseq 8:32 or resseq 34:43 or (resid...AA48 - 5353 - 58
14GLUGLUPROPRO(chain A and (resseq 8:32 or resseq 34:43 or (resid...AA56 - 7761 - 82
25THRTHRGLNGLN(chain B and (resseq 8:32 or resseq 34:46 or resseq 48:53 or resseq 56:77))BB8 - 3213 - 37
26ARGARGVALVAL(chain B and (resseq 8:32 or resseq 34:46 or resseq 48:53 or resseq 56:77))BB34 - 4539 - 50
27TYRTYRASPASP(chain B and (resseq 8:32 or resseq 34:46 or resseq 48:53 or resseq 56:77))BB48 - 5353 - 58
28GLUGLUPROPRO(chain B and (resseq 8:32 or resseq 34:46 or resseq 48:53 or resseq 56:77))BB56 - 7761 - 82

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Components

#1: Protein Aca1


Mass: 9413.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD30 (virus) / Gene: JBD30_036 / Production host: Escherichia coli (E. coli) / References: UniProt: L7P845
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate; 20% (w/v) PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.846→22.051 Å / Num. obs: 11611 / % possible obs: 99.3 % / Redundancy: 11.9 % / Biso Wilson estimate: 18.9268453641 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 4.54
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.642 / Num. unique obs: 1238 / CC1/2: 0.917 / CC star: 0.978 / Rrim(I) all: 0.677 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.847→22.051 Å / SU ML: 0.0959462699611 / Cross valid method: FREE R-VALUE / σ(F): 1.36224394051 / Phase error: 22.8627039952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.220288267463 549 4.72827491172 %
Rwork0.198589737173 11062 -
obs0.19967210604 11611 87.3927442421 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.7397606557 Å2
Refinement stepCycle: LAST / Resolution: 1.847→22.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 0 87 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008302059160571159
X-RAY DIFFRACTIONf_angle_d0.9690210493341571
X-RAY DIFFRACTIONf_chiral_restr0.0492966848609166
X-RAY DIFFRACTIONf_plane_restr0.00818768020274210
X-RAY DIFFRACTIONf_dihedral_angle_d21.9757463512725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.847-2.03240.256119723011070.1979440972761991X-RAY DIFFRACTION64.316370325
2.0324-2.32620.2280211218911290.1931148818582641X-RAY DIFFRACTION84.8132271892
2.3262-2.92970.217883613851410.2161595197053159X-RAY DIFFRACTION99.6376811594
2.9297-22.0510.2132189918251720.1916703022383271X-RAY DIFFRACTION99.9129425421
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)
13.23694583143-0.2137943310790.09698362579093.5195504327-0.2081878512761.735291596630.181519472246-0.15053929880.146053178843-0.0421494109610.0432218447214-0.664175752037-0.02557115816460.255292223943-0.1204291697220.0714842397019-0.00901586553508-0.01151206571820.115687145859-0.05647646027710.17407007660819.4543684701-4.70268614039-0.844678382344
22.875948958720.200721644785-0.6596720551974.694052622520.7486463849521.613570627480.1200383008270.08065499415240.246520184309-0.395579802269-0.0507908554150.358111430912-0.400787208204-0.475138228610.004247083713340.1562187078940.07398863807990.03445942233460.155320063353-0.02518039034740.1204635218372.258244124294.58081002845-1.54622447812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 77)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 77)

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