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- PDB-7k9b: Crystal structure of Bacillus halodurans OapB (native) at 1.2 A -

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Basic information

Entry
Database: PDB / ID: 7k9b
TitleCrystal structure of Bacillus halodurans OapB (native) at 1.2 A
ComponentsOLE-associated protein B
KeywordsRNA BINDING PROTEIN / ribonucleoprotein complex / OLE RNA
Function / homology
Function and homology information


ribosome / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein L14, KOW motif / SH3 type barrels. - #30 / SH3 type barrels. / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.202 Å
AuthorsYang, Y. / Breaker, R.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM022778 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex.
Authors: Yang, Y. / Harris, K.A. / Widner, D.L. / Breaker, R.R.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OLE-associated protein B
B: OLE-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8274
Polymers22,7562
Non-polymers712
Water5,531307
1
A: OLE-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4142
Polymers11,3781
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OLE-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4142
Polymers11,3781
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.918, 34.909, 49.811
Angle α, β, γ (deg.)90.000, 90.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OLE-associated protein B / OapB


Mass: 11378.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH0157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KGD7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM Tris-HCl (pH 8.5), 100 mM KCl, 10 mM MgCl2 and 30% polyethylene glycol (PEG) 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.2→47.96 Å / Num. obs: 50673 / % possible obs: 98.4 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Net I/σ(I): 17.8
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4791 / CC1/2: 0.973 / Rpim(I) all: 0.109 / Rrim(I) all: 0.191 / % possible all: 93

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.202→47.918 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1511 2530 5 %
Rwork0.1207 48114 -
obs0.1222 50644 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.88 Å2 / Biso mean: 17.094 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.202→47.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 2 311 1911
Biso mean--14.15 28.74 -
Num. residues----195
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2024-1.22550.17571250.13236788
1.2255-1.25060.17521400.1261267699
1.2506-1.27780.17851420.1275267999
1.2778-1.30750.1681410.1152268899
1.3075-1.34020.14061420.1097268699
1.3402-1.37640.14021400.108266899
1.3764-1.41690.15211400.1058268199
1.4169-1.46270.13631340.104257295
1.4627-1.51490.15311430.12704100
1.5149-1.57560.121410.09362691100
1.5756-1.64730.14221430.0959271899
1.6473-1.73420.14221400.10432678100
1.7342-1.84280.14321440.10642730100
1.8428-1.98510.13481390.1063263297
1.9851-2.18490.1311430.1063272099
2.1849-2.5010.12541430.11682716100
2.501-3.1510.16591440.1364274199
3.151-47.9180.18081460.1496276798

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