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- PDB-7oc9: Structure of Bdellovibrio bacteriovorus Bd0675 -

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Basic information

Entry
Database: PDB / ID: 7oc9
TitleStructure of Bdellovibrio bacteriovorus Bd0675
ComponentsBd0675
KeywordsUNKNOWN FUNCTION / Bdellovibrio Secretion Cryptic
Function / homologyTERTIARY-BUTYL ALCOHOL / Uncharacterized protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLovering, A.L. / Valdivia-Delgado, M.
Funding support Chile, 1items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)72180329 Chile
CitationJournal: Proteins / Year: 2021
Title: Target highlights in CASP14: Analysis of models by structure providers.
Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / ...Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / Fidelis, K. / Grinter, R. / Gupta, G.D. / Hartmann, M.D. / Hayes, C.S. / Heidebrecht, T. / Ilari, A. / Joachimiak, A. / Kim, Y. / Linares, R. / Lovering, A.L. / Lunin, V.V. / Lupas, A.N. / Makbul, C. / Michalska, K. / Moult, J. / Mukherjee, P.K. / Nutt, W.S. / Oliver, S.L. / Perrakis, A. / Stols, L. / Tainer, J.A. / Topf, M. / Tsutakawa, S.E. / Valdivia-Delgado, M. / Schwede, T.
History
DepositionApr 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 8, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bd0675
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1987
Polymers14,6911
Non-polymers5076
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint9 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.490, 69.670, 85.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein Bd0675


Mass: 14691.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd0675 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6MQ12
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 47% v/v MPD 2% t-Butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.5→42.43 Å / Num. obs: 25800 / % possible obs: 98.97 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04177 / Net I/σ(I): 24.27
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 1.887 / Num. unique obs: 2533 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→42.428 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 1260 4.88 %
Rwork0.1974 24540 -
obs0.1982 25800 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.62 Å2 / Biso mean: 47.4395 Å2 / Biso min: 25.67 Å2
Refinement stepCycle: final / Resolution: 1.5→42.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 96 74 1193
Biso mean--61.52 45.88 -
Num. residues----133
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5001-1.56010.34211360.3021267398
1.5601-1.63110.24681340.2634267498
1.6311-1.71710.28921700.2341263499
1.7171-1.82470.23121450.2219270599
1.8247-1.96560.25071230.2178271299
1.9656-2.16340.24281210.2076272699
2.1634-2.47640.23861630.20952722100
2.4764-3.11990.24111310.2172798100
3.1199-42.4280.18141370.17752896100

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