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- PDB-7k9d: Crystal structure of Bacillus halodurans OapB in complex with its... -

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Basic information

Entry
Database: PDB / ID: 7k9d
TitleCrystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal form I)
Components
  • OLE* RNA
  • OLE-associated protein B
KeywordsRNA-BINDING PROTEIN/RNA / ribonucleoprotein complex / OLE RNA / noncoding RNA / RNA / RNA-BINDING PROTEIN-RNA complex
Function / homologyRibosomal protein L14, KOW motif / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / COBALT HEXAMMINE(III) / RNA / RNA (> 10) / BH0157 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
Bacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.098 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* RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,16710
Polymers30,8442
Non-polymers1,3238
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-20 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.817, 98.817, 198.897
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-354-

HOH

31B-858-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein OLE-associated protein B / OapB


Mass: 11378.141 Da / Num. of mol.: 1
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: RNA chain OLE* RNA


Mass: 19465.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus halodurans C-125 (bacteria)

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Non-polymers , 4 types, 248 molecules

#3: 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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES (pH 7.0 to 7.5), 200 mM NH4Cl and 39 to 42.5% 2-Methyl-2,4-pentanediol (MPD)
PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.6058 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6058 Å / Relative weight: 1
ReflectionResolution: 2.098→41.84 Å / Num. obs: 42266 / % possible obs: 99.9 % / Redundancy: 9.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Net I/σ(I): 29.9
Reflection shellResolution: 2.098→2.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.211 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2175 / CC1/2: 0.816 / Rpim(I) all: 0.411 / Rrim(I) all: 1.28 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.098→41.832 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 1143 5.18 %
Rwork0.1619 40075 -
obs0.1636 42266 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.12 Å2 / Biso mean: 72.8179 Å2 / Biso min: 42.8 Å2
Refinement stepCycle: final / Resolution: 2.098→41.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 1288 65 240 2329
Biso mean--96.5 74.05 -
Num. residues----149
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.098-2.14360.41881180.33247298
2.1436-2.19340.31551760.30262491100
2.1934-2.24830.28431630.27432480100
2.2483-2.30910.27241740.26542460100
2.3091-2.3770.21121210.23562494100
2.377-2.45370.26231080.2182547100
2.4537-2.54140.23731450.23022506100
2.5414-2.64320.26981390.23562514100
2.6432-2.76340.2911200.23062515100
2.7634-2.90910.28171230.2222543100
2.9091-3.09130.15181280.17592523100
3.0913-3.32990.17321490.15732457100
3.3299-3.66480.20611410.14452544100
3.6648-4.19470.19151260.13162501100
4.1947-5.28320.16591240.12432534100
5.2832-41.8320.16791360.1412249499
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)
14.2896-0.11472.47747.9113-0.72789.21020.3052-0.404-0.02120.2185-0.1060.7035-0.2593-1.2282-0.17860.48440.05860.07550.59620.02750.5698-6.31136.35117.951
24.55841.5441.75453.6464-1.79536.93460.1844-0.3659-0.11130.4972-0.07490.15270.484-0.0489-0.12460.58260.11530.05550.54750.01010.5869-2.58634.987118.329
37.33120.31061.79691.6610.73398.5810.3412-1.0911-0.38951.0757-0.06880.35910.8287-0.5096-0.24710.85020.05310.05240.80920.08080.6583-0.34631.275130.287
43.7971-1.70840.13841.66080.4141-0.00940.07480.51730.3315-0.0815-0.09830.0461-0.0336-0.00990.00780.54870.0410.08330.78440.08640.6656-7.17441.19793.781
52.2983-2.0109-1.10982.92221.9651.30890.01220.094-0.06250.06680.0986-0.06930.081-0.018-0.09440.46260.08650.07910.59530.03890.58214.99634.298102.669
64.3964-0.66721.98953.9753-0.30914.85970.44650.8669-0.5837-0.88330.00090.08030.2528-0.1272-0.38980.71810.0360.02640.8522-0.0910.6488.7625.95385.826
74.8337-0.874-1.24052.47550.55693.43360.14530.5740.32370.1135-0.0978-0.01690.4567-1.034-0.04370.76610.16670.13421.03120.12250.61115.59235.62773.98
87.2732-0.8567-3.04724.60231.05712.76910.24062.25240.2203-1.1528-0.1747-0.1243-0.4446-0.52790.03730.93550.17570.17321.23410.06810.6463-2.01739.52682.228
97.71014.60841.31285.3968-1.37845.2733-0.78542.5670.9583-3.01360.6159-0.6711-1.36390.5059-0.04751.80790.43570.21862.07410.46171.0391-9.81649.86779.799
105.41831.5901-2.14286.4014-1.20257.95550.36922.0965-0.4218-1.0237-0.22420.61190.0746-1.1569-0.00720.51150.1517-0.01381.0430.00830.6425-13.00639.12191.855
111.42840.41132.82335.4464-1.78816.9154-0.49270.24860.24290.51480.2360.5736-0.38070.24020.31820.50690.10330.08440.71710.07690.7156-16.16847.103104.969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:40 )A6 - 40
2X-RAY DIFFRACTION2( CHAIN A AND RESID 41:65 )A41 - 65
3X-RAY DIFFRACTION3( CHAIN A AND RESID 66:94 )A66 - 94
4X-RAY DIFFRACTION4( CHAIN B AND RESID 485:494 )B485 - 494
5X-RAY DIFFRACTION5( CHAIN B AND RESID 495:509 )B495 - 509
6X-RAY DIFFRACTION6( CHAIN B AND RESID 510:514 )B510 - 514
7X-RAY DIFFRACTION7( CHAIN B AND RESID 515:524 )B515 - 524
8X-RAY DIFFRACTION8( CHAIN B AND RESID 525:529 )B525 - 529
9X-RAY DIFFRACTION9( CHAIN B AND RESID 530:534 )B530 - 534
10X-RAY DIFFRACTION10( CHAIN B AND RESID 535:539 )B535 - 539
11X-RAY DIFFRACTION11( CHAIN B AND RESID 540:543 )B540 - 543

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