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- PDB-2lw5: Solution structure of anti-CRISPR protein Acr30-35 from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2lw5
TitleSolution structure of anti-CRISPR protein Acr30-35 from Pseudomonas aeruginosa Phage JBD30
ComponentsACR30-35
KeywordsVIRAL PROTEIN / Phage / Pseudomonas aeruginosa / anti-CRISPR / CRISPR
Function / homologyViral Envelope Glycoprotein; domain 2 - #30 / : / Anti-CRISPR protein Acr30-35/AcrF1 / Viral Envelope Glycoprotein; domain 2 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsMaxwell, K.L. / Bondy-Denomy, J. / Davidson, A.R.
CitationJournal: To be Published
Title: Discovery of phage genes that allow evasion of the CRISPR/Cas bacterial immune system
Authors: Bondy-Denomy, J. / Maxwell, K.L. / Pawluk, A. / Davidson, A.R.
History
DepositionJul 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACR30-35


Theoretical massNumber of molelcules
Total (without water)8,8821
Polymers8,8821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ACR30-35


Mass: 8881.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD30 (virus) / Gene: JBD30_035 / Plasmid: pET15b-TVL / Production host: Escherichia coli (E. coli) / References: UniProt: L7P7M1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-13C HSQC
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1912D 1H-15N HSQC
11012D 1H-13C HSQC
11123D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aromatic
11323D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM [U-100% 13C; U-100% 15N] sodium phosphate, 200 mM [U-100% 13C; U-100% 15N] sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
225 mM [U-100% 13C; U-100% 15N] sodium phosphate, 200 mM [U-100% 13C; U-100% 15N] sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-2[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-3[U-100% 13C; U-100% 15N]2
200 mMsodium chloride-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 200 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGoddardrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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