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- PDB-5vqh: Crystal structure of the extended Tudor domain from BmPAPI in com... -

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Basic information

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


P granule organization / piRNA processing / P granule / spermatogenesis / mitochondrial outer membrane / RNA binding
Similarity search - Function
: / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Type-1 KH domain profile. ...: / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Type-1 KH domain profile. / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / K Homology domain, type 1 superfamily / SH3 type barrels. / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N3, N4-DIMETHYLARGININE / Tudor and KH domain-containing protein homolog
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Mar 10, 2021Group: Derived calculations / Category: struct_conn
Revision 1.4Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,3114
Polymers53,9062
Non-polymers4052
Water2,756153
1
A: Tudor and KH domain-containing protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1552
Polymers26,9531
Non-polymers2021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tudor and KH domain-containing protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1552
Polymers26,9531
Non-polymers2021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.030, 66.030, 224.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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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 / 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: Chemical ChemComp-2MR / N3, N4-DIMETHYLARGININE


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H18N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
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 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→39.61 Å / Num. obs: 18600 / % possible obs: 92.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6867 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VQG

5vqg


Resolution: 2.4→39.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.461 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.289 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 878 4.7 %RANDOM
Rwork0.195 ---
obs0.198 17693 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 28 153 3394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193330
X-RAY DIFFRACTIONr_bond_other_d0.0010.023058
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9324530
X-RAY DIFFRACTIONr_angle_other_deg0.77436971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69723.212165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05215498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
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_it3.1084.3931637
X-RAY DIFFRACTIONr_mcbond_other3.1064.3921636
X-RAY DIFFRACTIONr_mcangle_it4.7736.5592035
X-RAY DIFFRACTIONr_mcangle_other4.7726.5612036
X-RAY DIFFRACTIONr_scbond_it3.6114.8021693
X-RAY DIFFRACTIONr_scbond_other3.6034.81693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8397.0412493
X-RAY DIFFRACTIONr_long_range_B_refined8.17935.3963759
X-RAY DIFFRACTIONr_long_range_B_other8.17735.3893714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 56 -
Rwork0.344 1347 -
obs--94.35 %

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