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- PDB-3wbm: Crystal Structure of protein-RNA complex -

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Basic information

Entry
Database: PDB / ID: 3wbm
TitleCrystal Structure of protein-RNA complex
Components
  • DNA/RNA-binding protein Alba 1
  • RNA (25-MER)
KeywordsRNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / DNA/RNA BINDING / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nuclease activity / chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / DNA/RNA-binding protein Alba 1
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDing, J. / Wang, D.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea.
Authors: Guo, L. / Ding, J. / Guo, R. / Hou, Y. / Wang, D.C. / Huang, L.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Source and taxonomy / Category: citation / entity_src_gen / pdbx_entity_src_syn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Nov 8, 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: DNA/RNA-binding protein Alba 1
B: DNA/RNA-binding protein Alba 1
C: DNA/RNA-binding protein Alba 1
D: DNA/RNA-binding protein Alba 1
X: RNA (25-MER)
Y: RNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)58,3056
Polymers58,3056
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-55 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.890, 69.760, 48.130
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-60-

PHE

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Components

#1: Protein
DNA/RNA-binding protein Alba 1 / Ssh10b


Mass: 10601.442 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus shibatae (archaea) / Strain: 2286 / Gene: albA1, ssh10b / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60848
#2: RNA chain RNA (25-MER)


Mass: 7949.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% (v/v) PEG 5000 MME, 100mM Bis-Tris, 200mM sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9642 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9642 Å / Relative weight: 1
ReflectionResolution: 2→47.84 Å / Num. all: 37892 / Num. obs: 37589 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.85 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 11
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5444 / Rsym value: 0.407 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0X

1h0x


Resolution: 2→43.804 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8165 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1882 5.01 %RANDOM
Rwork0.212 ---
all0.2139 37900 --
obs0.2139 37582 99.16 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.773 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 110.96 Å2 / Biso mean: 40.5243 Å2 / Biso min: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.2402 Å2-0 Å21.7172 Å2
2---0.6102 Å2-0 Å2
3---5.8504 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→43.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 1050 0 310 4024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033851
X-RAY DIFFRACTIONf_angle_d0.6725420
X-RAY DIFFRACTIONf_dihedral_angle_d10.7921645
X-RAY DIFFRACTIONf_chiral_restr0.048714
X-RAY DIFFRACTIONf_plane_restr0.004493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.05410.30571440.2495270799
2.0541-2.11450.28931400.2273273699
2.1145-2.18280.26371370.2221272599
2.1828-2.26080.28211450.2166269599
2.2608-2.35130.26871490.2164273899
2.3513-2.45830.3051350.2341272499
2.4583-2.58790.29281470.2307276499
2.5879-2.750.25671280.23552764100
2.75-2.96230.28161500.23112747100
2.9623-3.26030.26191440.222780100
3.2603-3.73190.2391690.20522748100
3.7319-4.70090.20471310.17792802100
4.7009-43.81460.22311630.2092277098

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