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- PDB-5vy1: Crystal structure of the extended Tudor domain from BmPAPI -

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Basic information

Entry
Database: PDB / ID: 5vy1
TitleCrystal structure of the extended Tudor domain from BmPAPI
ComponentsTudor and KH domain-containing protein homolog
KeywordsRNA BINDING PROTEIN / BmPAPI / Tudor / sDMA
Function / homology
Function and homology information


piRNA processing / spermatogenesis / mitochondrial outer membrane / cell differentiation / RNA binding
Similarity search - Function
: / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 ...: / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tudor and KH domain-containing protein homolog
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsHubbard, P.A. / Pan, X. / McNally, R. / Ohtaki, A. / Honda, S. / Kirino, Y. / Murali, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106047 United States
CitationJournal: To Be Published
Title: Structural studies of the Tudor domain from the Bombyx homolog of Drosophila PAPI: Implication to piRNA biogenesis
Authors: Hubbard, P.A. / Pan, X. / McNally, R. / Ohtaki, A. / Honda, S. / Kirino, Y. / Murali, R.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Assembly

Deposited unit
A: Tudor and KH domain-containing protein homolog
B: Tudor and KH domain-containing protein homolog


Theoretical massNumber of molelcules
Total (without water)53,9062
Polymers53,9062
Non-polymers00
Water0
1
A: Tudor and KH domain-containing protein homolog


Theoretical massNumber of molelcules
Total (without water)26,9531
Polymers26,9531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tudor and KH domain-containing protein homolog


Theoretical massNumber of molelcules
Total (without water)26,9531
Polymers26,9531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.717, 65.717, 225.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tudor and KH domain-containing protein homolog / Partner of PIWIs protein / BmPAPI


Mass: 26953.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: PAPI / Production host: Escherichia coli (E. coli) / References: UniProt: H9JD76

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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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.95 M ammonium sulfate, 50 mM sodium acetate, pH 5.5 and 5% glucose.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.05→19.5 Å / Num. obs: 8655 / % possible obs: 87.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 5.9
Reflection shellResolution: 3.05→3.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1274 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VQG

5vqg


Resolution: 3.05→19.064 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.53
RfactorNum. reflection% reflection
Rfree0.296 432 5 %
Rwork0.2532 --
obs0.2554 8647 85.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.05→19.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 0 0 3011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023083
X-RAY DIFFRACTIONf_angle_d0.6544203
X-RAY DIFFRACTIONf_dihedral_angle_d13.0251050
X-RAY DIFFRACTIONf_chiral_restr0.025470
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.48910.3891410.32262750X-RAY DIFFRACTION88
3.4891-4.3870.27221350.23932746X-RAY DIFFRACTION87
4.387-19.06390.27141560.22972719X-RAY DIFFRACTION82

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