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- PDB-7k9c: Crystal structure of Bacillus halodurans OapB (iodine-derivative)... -

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Basic information

Entry
Database: PDB / ID: 7k9c
TitleCrystal structure of Bacillus halodurans OapB (iodine-derivative) at 1.0 A
ComponentsOLE-associated protein B
KeywordsRNA / ribonucleoprotein complex / OLE RNA / RNA BINDING PROTEIN
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
IODIDE ION / BH0157 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1 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)24,78718
Polymers22,7562
Non-polymers2,03016
Water4,179232
1
A: OLE-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1407
Polymers11,3781
Non-polymers7616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OLE-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,64711
Polymers11,3781
Non-polymers1,26910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.904, 34.912, 49.637
Angle α, β, γ (deg.)90.000, 90.150, 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.82 Å3/Da / Density % sol: 32.56 %
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-C / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1→49.7 Å / Num. obs: 85634 / % possible obs: 96.4 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.033 / Rrim(I) all: 0.069 / Net I/σ(I): 11.2
Reflection shellResolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8108 / CC1/2: 0.573 / Rpim(I) all: 0.519 / Rrim(I) all: 1.072 / % possible all: 92

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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→49.637 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1628 4278 5 %
Rwork0.148 81337 -
obs0.1488 85615 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.09 Å2 / Biso mean: 15.4759 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1→49.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 17 235 1846
Biso mean--18.76 25.54 -
Num. residues----194
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1-1.01130.32061340.2959255791
1.0113-1.02320.26581350.2845255592
1.0232-1.03560.25851360.2725259193
1.0356-1.04880.2161370.2588260193
1.0488-1.06260.24451390.2343265593
1.0626-1.07710.22771380.229262395
1.0771-1.09250.21821380.2179262694
1.0925-1.10880.20231400.2028266096
1.1088-1.12610.21071420.1871270295
1.1261-1.14460.20181430.1748271198
1.1446-1.16430.16431410.1632268596
1.1643-1.18550.19181450.1531274798
1.1855-1.20830.16261430.1513272096
1.2083-1.2330.15991430.1525271498
1.233-1.25980.14881440.1416273897
1.2598-1.28910.15281440.1383274698
1.2891-1.32130.15351420.1312268897
1.3213-1.35710.13471410.122268696
1.3571-1.3970.13031460.119276398
1.397-1.44210.11391470.1177278999
1.4421-1.49370.1381440.118275098
1.4937-1.55350.12721470.1157279299
1.5535-1.62420.10541450.1113274399
1.6242-1.70980.12611470.1204279999
1.7098-1.81690.14171430.1193270896
1.8169-1.95720.13071420.1246271296
1.9572-2.15420.14711480.1282281599
2.1542-2.46590.17441510.14122853100
2.4659-3.10670.18141480.1535281699
3.1067-49.6370.17761450.1636279295

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