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- PDB-1q7f: Brain Tumor NHL domain -

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Basic information

Entry
Database: PDB / ID: 1q7f
TitleBrain Tumor NHL domain
Componentsbrain tumor CG10719-PA
KeywordsTRANSLATION / brat / NHL domain / NHL repeat / beta-propeller
Function / homology
Function and homology information


asymmetric neuroblast division resulting in ganglion mother cell formation / ganglion mother cell fate determination / neuroblast development / neuroblast fate determination / segmentation / regulation of synaptic assembly at neuromuscular junction / asymmetric cell division / ventral cord development / basal cortex / regulation of neuroblast proliferation ...asymmetric neuroblast division resulting in ganglion mother cell formation / ganglion mother cell fate determination / neuroblast development / neuroblast fate determination / segmentation / regulation of synaptic assembly at neuromuscular junction / asymmetric cell division / ventral cord development / basal cortex / regulation of neuroblast proliferation / neuroblast differentiation / Neutrophil degranulation / apical cortex / regulation of synaptic vesicle endocytosis / negative regulation of neuroblast proliferation / oogenesis / rRNA transcription / regulation of neurogenesis / neuroblast proliferation / translation regulator activity / translation repressor activity / mRNA 3'-UTR binding / brain development / neuron differentiation / regulation of translation / negative regulation of translation / negative regulation of cell population proliferation / negative regulation of gene expression / neuronal cell body / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like ...: / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsEdwards, T.A. / Wilkinson, B.D. / Wharton, R.P. / Aggarwal, A.K.
CitationJournal: Genes Dev. / Year: 2003
Title: Model of the Brain Tumor-Pumilio translation repressor complex
Authors: Edwards, T.A. / Wilkinson, B.D. / Wharton, R.P. / Aggarwal, A.K.
History
DepositionAug 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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

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Assembly

Deposited unit
A: brain tumor CG10719-PA
B: brain tumor CG10719-PA


Theoretical massNumber of molelcules
Total (without water)64,8442
Polymers64,8442
Non-polymers00
Water11,890660
1
A: brain tumor CG10719-PA


Theoretical massNumber of molelcules
Total (without water)32,4221
Polymers32,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: brain tumor CG10719-PA


Theoretical massNumber of molelcules
Total (without water)32,4221
Polymers32,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.770, 94.580, 130.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein brain tumor CG10719-PA / NHL


Mass: 32421.926 Da / Num. of mol.: 2 / Fragment: Brain Tumor NHL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: brain tumor / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8MQJ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 55% amm PO4 5% MPD, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mg/mlprotein1drop
220 mMBis-Tris1drop
350 mM1dropNaCl
41 mMdithiothreitol1droppH6
553 %di-basic ammonium phosphate1reservoir
64 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 42070 / Num. obs: 35583 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.94 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 7.3 / % possible all: 68.7
Reflection
*PLUS
Num. obs: 42132 / % possible obs: 84.1 % / Num. measured all: 250484
Reflection shell
*PLUS
% possible obs: 68.7 % / Mean I/σ(I) obs: 7.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1425 3.4 %RANDOM
Rwork0.2 ---
obs0.2002 35583 84.6 %-
all-42070 --
Displacement parametersBiso mean: 28 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 0 660 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00623
X-RAY DIFFRACTIONc_angle_d1.358
X-RAY DIFFRACTIONc_mcbond_it1.5041.5
X-RAY DIFFRACTIONc_scbond_it2.1922
X-RAY DIFFRACTIONc_mcangle_it2.3082
X-RAY DIFFRACTIONc_scangle_it3.232.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor Rwork: 0.2002
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00623
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.358

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