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- PDB-6be0: AvrA delL154 with IP6, CoA -

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Basic information

Entry
Database: PDB / ID: 6be0
TitleAvrA delL154 with IP6, CoA
ComponentsAvrA
KeywordsTRANSFERASE / acetyltransferase / YopJ family / IP6 / bacterial effector
Function / homologySerine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / acyltransferase activity / COENZYME A / INOSITOL HEXAKISPHOSPHATE / AvrA
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.438 Å
AuthorsLabriola, J.M. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Biochemistry / Year: 2018
Title: Structural Analysis of the Bacterial Effector AvrA Identifies a Critical Helix Involved in Substrate Recognition.
Authors: Labriola, J.M. / Zhou, Y. / Nagar, B.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2393
Polymers33,8121
Non-polymers1,4282
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.931, 62.931, 187.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AvrA


Mass: 33811.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 4/74) (bacteria)
Strain: 4/74 / Gene: avrA, STM474_3004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E8XKZ3
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 8.5% PEG8000, 15% ethylene glycol, 100mM MES pH 5.6 - 5.8
PH range: 5.6 - 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.438→50 Å / Num. obs: 25168 / % possible obs: 99.8 % / Redundancy: 10.6 % / Net I/σ(I): 31.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLP

5klp


Resolution: 2.438→41.083 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1275 5.07 %
Rwork0.187 --
obs0.1892 25168 81.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.438→41.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 63 65 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032211
X-RAY DIFFRACTIONf_angle_d0.6492997
X-RAY DIFFRACTIONf_dihedral_angle_d11.991826
X-RAY DIFFRACTIONf_chiral_restr0.026336
X-RAY DIFFRACTIONf_plane_restr0.002374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4382-2.53580.3173370.2749658X-RAY DIFFRACTION20
2.5358-2.65120.2947700.25041315X-RAY DIFFRACTION41
2.6512-2.79090.28611330.25482478X-RAY DIFFRACTION75
2.7909-2.96570.29661670.24673123X-RAY DIFFRACTION95
2.9657-3.19460.29831740.25473281X-RAY DIFFRACTION100
3.1946-3.51590.26491730.21093263X-RAY DIFFRACTION100
3.5159-4.02430.19871750.18073246X-RAY DIFFRACTION100
4.0243-5.06870.17661740.13653272X-RAY DIFFRACTION100
5.0687-41.08840.20511720.14293257X-RAY DIFFRACTION99
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)
15.76681.0993.30284.04772.46215.72650.4369-0.053-0.6954-0.0936-0.4090.0030.7426-0.4686-0.07780.656-0.14850.00820.347-0.04370.3133-24.8746-2.7873-19.7379
21.58580.8832-0.5152.4101-0.34671.50540.02090.11150.1658-0.03350.0237-0.0953-0.06930.0338-0.00070.4461-0.26170.06680.3170.05230.3886-17.096415.0216-9.8905
32.07460.540.24021.57990.0640.53830.0127-0.07450.21410.1233-0.06230.002-0.058-0.00390.03780.509-0.35450.05410.2031-0.03290.3737-24.281316.9944-0.412
44.36174.91422.48155.55032.85681.64720.3986-0.5379-0.20120.6096-0.3346-0.02050.0124-0.1297-0.07010.5451-0.29490.10910.47190.10970.4824-30.8188.3167.7545
52.37910.5724-0.06792.88030.15132.20680.2616-0.45410.20750.5309-0.24810.17390.0616-0.08920.00970.4606-0.22220.04320.3423-0.02410.4139-30.69716.65933.7407
62.9380.299-0.00255.07842.3372.57110.0475-0.29790.35010.2686-0.23450.67070.0115-0.24960.17450.483-0.2028-0.0070.2894-0.02280.4364-34.233717.2714-5.3278
73.36890.49440.17914.15452.18685.56160.0090.72640.1433-0.6701-0.11091.0822-0.1357-1.01380.14780.4405-0.0857-0.20480.44090.01640.531-41.029216.1316-17.7516
85.1362-2.33141.30213.27211.30335.0039-0.28370.6516-0.375-0.68220.19810.51410.1175-0.34260.09240.6237-0.2163-0.07880.3629-0.03210.2877-30.00014.993-24.2005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 256 )
8X-RAY DIFFRACTION8chain 'A' and (resid 257 through 301 )

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