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- PDB-9lrg: Crystal Structure of Thermus thermophilus KhpB/EloR -

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Basic information

Entry
Database: PDB / ID: 9lrg
TitleCrystal Structure of Thermus thermophilus KhpB/EloR
ComponentsProbable DNA/RNA-binding protein (Jag-related protein)
KeywordsRNA BINDING PROTEIN / RNA-binding protein / KH domain / R3H domain / Thermus thermophilus
Function / homology
Function and homology information


RNA binding / cytoplasm
Similarity search - Function
RNA-binding protein KhpB, R3H domain / Jag, KH domain / RNA-binding protein KhpB / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / K homology domain-like, alpha/beta
Similarity search - Domain/homology
Probable DNA/RNA-binding protein (Jag-related protein)
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsFukui, K. / Murakawa, T. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: KH-R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB.
Authors: Fukui, K. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionJan 31, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Probable DNA/RNA-binding protein (Jag-related protein)


Theoretical massNumber of molelcules
Total (without water)21,0441
Polymers21,0441
Non-polymers00
Water00
1
AA: Probable DNA/RNA-binding protein (Jag-related protein)

AA: Probable DNA/RNA-binding protein (Jag-related protein)


Theoretical massNumber of molelcules
Total (without water)42,0882
Polymers42,0882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.011, 47.011, 265.782
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Probable DNA/RNA-binding protein (Jag-related protein) / KhpB/EloR


Mass: 21044.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0442 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q5SL51
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.0M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→36.99 Å / Num. obs: 3900 / % possible obs: 95.9 % / Redundancy: 20 % / Biso Wilson estimate: 62.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.029 / Rrim(I) all: 0.145 / Net I/σ(I): 41.3
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 15 % / Rmerge(I) obs: 0.275 / Num. unique obs: 349 / CC1/2: 0.995 / Rpim(I) all: 0.052 / Rrim(I) all: 0.145 / % possible all: 96.9

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Processing

Software
NameVersionClassification
Coot0.9.8.92model building
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→36.99 Å / SU ML: 0.2329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 189 4.85 %
Rwork0.2505 3711 -
obs0.2515 3900 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.73 Å2
Refinement stepCycle: LAST / Resolution: 2.99→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 0 0 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241128
X-RAY DIFFRACTIONf_angle_d0.46331530
X-RAY DIFFRACTIONf_chiral_restr0.0385174
X-RAY DIFFRACTIONf_plane_restr0.0038204
X-RAY DIFFRACTIONf_dihedral_angle_d11.2226418
LS refinement shellResolution: 2.99→10 Å
RfactorNum. reflection% reflection
Rfree0.2702 189 -
Rwork0.2505 3711 -
obs--95.99 %
Refinement TLS params.Method: refined / Origin x: 17.2042883937 Å / Origin y: 10.665931963 Å / Origin z: -12.8094055649 Å
111213212223313233
T0.490210164294 Å2-0.0818640788349 Å2-0.0858623093547 Å2-0.424480053406 Å2-0.0326276852141 Å2--0.266590164565 Å2
L5.08903029373 °2-2.89081469069 °2-2.33312342831 °2-3.80873431942 °20.101237811162 °2--1.7368390204 °2
S-0.043112220476 Å °0.296571311812 Å °-0.118183254512 Å °0.239293134278 Å °0.00820822267136 Å °-0.106571627706 Å °0.081580418469 Å °-0.325517968075 Å °0.0645552266008 Å °
Refinement TLS groupSelection details: all

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