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

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Basic information

Entry
Database: PDB / ID: 7kkv
TitleCrystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (native, 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 / 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
RNA / RNA (> 10) / BH0157 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
Bacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionOct 28, 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 1.2Oct 18, 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: OLE-associated protein B
B: OLE* RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2496
Polymers30,8442
Non-polymers4054
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-27 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.947, 98.947, 197.852
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-357-

HOH

21B-861-

HOH

31B-903-

HOH

41B-917-

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, 282 molecules

#3: Chemical ChemComp-MPD / (4S)-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


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.2 %
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: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.95→42.84 Å / Num. obs: 27246 / % possible obs: 99.1 % / Redundancy: 4.5 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.015 / Rrim(I) all: 0.033 / Net I/σ(I): 20.5 / Num. measured all: 123752
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-24.71.71873918550.490.8671.922196.9
8.93-42.844.10.0212843150.9990.0120.02365.795.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K9D

7k9d


Resolution: 2→41.875 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1261 5 %
Rwork0.1693 23979 -
obs0.1703 25240 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.96 Å2 / Biso mean: 75.9925 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2→41.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 1288 25 278 2327
Biso mean--73.67 75.2 -
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 (%)
2-2.08010.3261380.3225260398
2.0801-2.17480.30111370.2739260798
2.1748-2.28940.28621380.2509263799
2.2894-2.43280.24551390.2313264599
2.4328-2.62060.27531390.2312264599
2.6206-2.88430.31471400.2427266399
2.8843-3.30150.18081400.1634268699
3.3015-4.1590.14191420.1454269499
4.159-41.8750.17061480.1451279999
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)
12.1929-0.77581.5147.6135-0.81537.46240.3051-1.3417-0.24330.48920.17031.16350.5097-1.6069-0.8540.5741-0.00630.0970.86540.060.6667-9.227833.9047121.1426
25.70821.2727-0.08543.9501-1.21244.08060.17750.6374-0.2117-0.7590.1239-0.31261.51290.3744-0.12730.71950.2006-0.02930.6088-0.03730.5978-1.814830.6022108.6724
34.48251.28481.33033.6351-0.53444.40110.35150.07260.66790.3373-0.2946-0.0677-0.2445-0.1629-0.02210.59780.16770.08630.62850.01190.5416-2.042539.1537118.7079
43.68250.61411.49432.2809-0.98664.91490.02220.04910.23030.0560.13440.57880.3755-0.9647-0.22090.49040.10.11330.6520.05230.5997-8.607634.8552116.9352
53.18431.65921.91887.36930.78074.29670.2088-1.65570.7661.6143-0.11580.79140.1058-0.4891-0.06170.95810.0690.11951.0076-0.03510.6683-1.055837.7808133.0261
66.10460.2262.28978.09281.98117.46180.7103-1.1059-0.59751.2528-0.27560.49561.7054-0.1973-0.3570.94950.0574-0.05770.67030.11180.77010.405225.4692126.5985
72.9882-1.02610.29121.25530.19430.0882-0.09470.52440.25610.05650.1242-0.05360.0748-0.0987-0.06970.46520.11070.09620.76970.07770.62430.230337.140998.6491
81.97380.077-1.35280.6054-0.92712.11580.3010.9850.4363-0.13090.14280.1166-0.2187-1.016-0.39770.68170.19410.09491.02260.06280.614413.406632.315977.621
94.5576-2.3238-1.60643.8121-1.02952.440.49971.76620.8795-1.01850.0114-0.0151-0.2933-0.9412-0.65521.00210.34450.26891.60260.21640.7747-1.616238.910581.9597
106.40590.3286-2.29680.48980.54261.7468-0.76682.26941.7727-2.31760.9191-0.1259-0.53671.7843-0.0621.59160.24430.33792.62860.79451.5794-8.688949.064178.9736
112.89441.16680.83911.66440.734.43030.44541.22110.4046-0.3179-0.0810.29410.1087-0.50420.07510.540.16060.05091.02850.09330.7017-12.836938.987391.2233
122.33361.10031.44311.5362-0.33192.1794-0.40530.43221.05580.43260.15480.7034-0.0771-0.35710.21180.43910.1080.05880.8260.04190.7884-16.232147.0114104.4675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 16 )A6 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 24 )A17 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 50 )A25 - 50
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 65 )A51 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 79 )A66 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 94 )A80 - 94
7X-RAY DIFFRACTION7chain 'B' and (resid 485 through 509 )B485 - 509
8X-RAY DIFFRACTION8chain 'B' and (resid 510 through 524 )B510 - 524
9X-RAY DIFFRACTION9chain 'B' and (resid 525 through 529 )B525 - 529
10X-RAY DIFFRACTION10chain 'B' and (resid 530 through 534 )B530 - 534
11X-RAY DIFFRACTION11chain 'B' and (resid 535 through 539 )B535 - 539
12X-RAY DIFFRACTION12chain 'B' and (resid 540 through 543 )B540 - 543

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