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- PDB-7cfb: Drosophila melanogaster Krimper eTud1 apo structure -

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Basic information

Entry
Database: PDB / ID: 7cfb
TitleDrosophila melanogaster Krimper eTud1 apo structure
ComponentsFI20010p1
KeywordsGENE REGULATION / piRNA ampilication / gene silencing
Function / homology
Function and homology information


negative regulation of oskar mRNA translation / oocyte karyosome formation / secondary piRNA processing / oocyte dorsal/ventral axis specification / P granule / perinuclear region of cytoplasm / metal ion binding
Similarity search - Function
: / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / SNase-like, OB-fold superfamily
Similarity search - Domain/homology
Tudor domain-containing protein krimp
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, H. / Li, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870755 China
CitationJournal: Nat Commun / Year: 2021
Title: Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex.
Authors: Huang, X. / Hu, H. / Webster, A. / Zou, F. / Du, J. / Patel, D.J. / Sachidanandam, R. / Toth, K.F. / Aravin, A.A. / Li, S.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FI20010p1
B: FI20010p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3573
Polymers54,2612
Non-polymers961
Water3,729207
1
A: FI20010p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2272
Polymers27,1311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area10370 Å2
MethodPISA
2
B: FI20010p1


Theoretical massNumber of molelcules
Total (without water)27,1311
Polymers27,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.458, 87.692, 90.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FI20010p1 / Krimper


Mass: 27130.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: krimp, Dmel\CG15707, KRIMP, Krimp, krimp-RA, mtc, CG15707, Dmel_CG15707
Production host: Escherichia coli (E. coli) / References: UniProt: A1ZAC4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 1.26 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28640 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.062 / Rrim(I) all: 0.148 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2795 / CC1/2: 0.727 / CC star: 0.918 / Rpim(I) all: 0.472 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CFC

7cfc


Resolution: 2.1→31.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1408 4.96 %
Rwork0.204 26995 -
obs0.2049 28403 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 39.3454 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 2.1→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 5 207 3274
Biso mean--37.56 42.97 -
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.17470.31091220.2562263898
2.1747-2.26180.36141390.3348262798
2.2618-2.36470.28421460.2656254195
2.3647-2.48930.26181550.24312675100
2.4893-2.64520.30361300.24122719100
2.6452-2.84930.23281160.21932722100
2.8493-3.13580.23231640.21542700100
3.1358-3.5890.21891680.1932710100
3.589-4.51960.1691370.17042772100
4.5196-31.440.17431310.1687289199

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