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- PDB-3n89: KH domains -

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Basic information

Entry
Database: PDB / ID: 3n89
TitleKH domains
ComponentsDefective in germ line development protein 3, isoform a
KeywordsCELL CYCLE / KH domains / RNA binding / germline development
Function / homology
Function and homology information


germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / negative regulation of binding / nematode larval development / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division ...germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / negative regulation of binding / nematode larval development / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division / positive regulation of meiotic nuclear division / positive regulation of multicellular organism growth / P granule / embryo development ending in birth or egg hatching / : / RNA polymerase complex / mitotic cytokinesis / positive regulation of mitotic nuclear division / meiotic cell cycle / mRNA processing / regulation of translation / spermatogenesis / protein domain specific binding / positive regulation of gene expression / perinuclear region of cytoplasm / RNA binding / cytoplasm
Similarity search - Function
TATA-Binding Protein - #270 / GLD-3, KH5 domain / : / : / GLD-3 KH domain 5 / GLD-3, KH3 domain / TATA-Binding Protein - #210 / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defective in germ line development protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.789 Å
AuthorsNakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E.
CitationJournal: Rna / Year: 2010
Title: Four KH domains of the C. elegans Bicaudal-C ortholog GLD-3 form a globular structural platform.
Authors: Nakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defective in germ line development protein 3, isoform a
B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)85,7542
Polymers85,7542
Non-polymers00
Water77543
1
A: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)42,8771
Polymers42,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)42,8771
Polymers42,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Defective in germ line development protein 3, isoform a

B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)85,7542
Polymers85,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.504, 102.241, 83.608
Angle α, β, γ (deg.)90.00, 119.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Defective in germ line development protein 3, isoform a


Mass: 42876.961 Da / Num. of mol.: 2 / Fragment: UNP residues 88-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-3, T07F8.3 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold pLyS / References: UniProt: Q95ZK7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammoniumsulfate, Hepes, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.979
SYNCHROTRONSLS X06SA21
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMar 26, 2009
MARMOSAIC 225 mm CCD2CCDFeb 25, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled fixed-exit Si(111) monochromatorMADMx-ray1
2LN2 cooled fixed-exit Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
211
ReflectionResolution: 2.79→48.1 Å / Num. obs: 28664 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.134 / Net I/σ(I): 8.61
Reflection shellResolution: 2.79→3.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7600 / Rsym value: 0.593

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.789→48.113 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1489 5.1 %RANDOM
Rwork0.259 ---
all-28616 --
obs-28617 97.8 %-
Solvent computationBsol: 50.023 Å2
Displacement parametersBiso max: 59.8 Å2 / Biso mean: 31.207 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.754 Å20 Å23.445 Å2
2---0.579 Å20 Å2
3---2.333 Å2
Refinement stepCycle: LAST / Resolution: 2.789→48.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 0 43 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.214
X-RAY DIFFRACTIONc_mcbond_it1.1921.5
X-RAY DIFFRACTIONc_scbond_it1.7122
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scangle_it2.3762.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramCNS_TOPPAR:ion.top

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