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

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Basic information

Entry
Database: PDB / ID: 5vqg
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: 2.6 Å
AuthorsHubbard, P.A. / Pan, X. / Ohtaki, A. / McNally, R. / 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. / Ohtaki, A. / McNally, R. / Honda, S. / Kirino, Y. / Murali, R.
History
DepositionMay 8, 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


Theoretical massNumber of molelcules
Total (without water)26,9531
Polymers26,9531
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.560, 63.560, 100.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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.: 1 / Fragment: UNP residues 245-462
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 1% PEG 8,000, 50 mM MES, pH 5.5, 100 mM KCl and 10 mM MgCl2

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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: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→31.78 Å / Num. obs: 7535 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 915 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDR

3fdr


Resolution: 2.6→31.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.681 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.858 / ESU R Free: 0.352 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27705 419 5.5 %RANDOM
Rwork0.20141 ---
obs0.20571 7150 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.595 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.6→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 56 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191612
X-RAY DIFFRACTIONr_bond_other_d0.0010.021459
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9232196
X-RAY DIFFRACTIONr_angle_other_deg0.77733317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30823.02676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83715230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3243.505808
X-RAY DIFFRACTIONr_mcbond_other2.3153.504807
X-RAY DIFFRACTIONr_mcangle_it3.8735.2341003
X-RAY DIFFRACTIONr_mcangle_other3.8725.2351004
X-RAY DIFFRACTIONr_scbond_it2.4083.723804
X-RAY DIFFRACTIONr_scbond_other2.4073.724804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0325.4931193
X-RAY DIFFRACTIONr_long_range_B_refined6.50228.1311762
X-RAY DIFFRACTIONr_long_range_B_other6.46428.1821746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 33 -
Rwork0.359 533 -
obs--100 %

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