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- PDB-6d69: Crystal Structure of the NHL Repeat Region of D. melanogaster Thin -

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Basic information

Entry
Database: PDB / ID: 6d69
TitleCrystal Structure of the NHL Repeat Region of D. melanogaster Thin
ComponentsNHL Repeat Region of D. melanogaster Thin
KeywordsPROTEIN BINDING / protein-protein interaction / beta-propeller / limb girdle muscular dystrophy type 2H
Function / homology
Function and homology information


muscle cell development => GO:0055001 / myofibril assembly / muscle cell cellular homeostasis / striated muscle contraction / translation repressor activity / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process ...muscle cell development => GO:0055001 / myofibril assembly / muscle cell cellular homeostasis / striated muscle contraction / translation repressor activity / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of translation / protein ubiquitination / zinc ion binding
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Six-bladed beta-propeller, TolB-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.601 Å
AuthorsRamyar, K.X. / McWhorter, W.J. / Geisbrecht, B.V.
CitationJournal: Elife / Year: 2020
Title: DrosophilaTRIM32 cooperates with glycolytic enzymes to promote cell growth.
Authors: Bawa, S. / Brooks, D.S. / Neville, K.E. / Tipping, M. / Sagar, M.A. / Kollhoff, J.A. / Chawla, G. / Geisbrecht, B.V. / Tennessen, J.M. / Eliceiri, K.W. / Geisbrecht, E.R.
History
DepositionApr 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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: NHL Repeat Region of D. melanogaster Thin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2562
Polymers33,1641
Non-polymers921
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.727, 132.727, 49.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NHL Repeat Region of D. melanogaster Thin / Thin / isoform A / isoform B


Mass: 33163.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tn, abba, CG15105, Dmel_CG15105 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7JUV6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.95 Å3/Da / Density % sol: 68.89 % / Description: rod-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES (pH 7.8) 0.2 M sodium chloride 25% (w/v) peg-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15485 / % possible obs: 99 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.19 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.069 / Net I/σ(I): 14.36
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.6940.6814041.163191.9
2.69-2.85.20.52215261.132198.5
2.8-2.936.70.41415611.114199.7
2.93-3.087.60.33715561.0811100
3.08-3.2880.23315441.067199.9
3.28-3.5380.14515551.108199.9
3.53-3.888.10.1215531.011199.9
3.88-4.4580.08715751.063199.9
4.45-5.67.90.06215781.081199.9
5.6-507.70.05216330.966199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q7F

1q7f


Resolution: 2.601→43.445 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.2194 1533 9.91 %
Rwork0.186 --
obs0.1894 15474 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.41 Å2 / Biso mean: 37.7815 Å2 / Biso min: 16.5 Å2
Refinement stepCycle: final / Resolution: 2.601→43.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 6 85 2349
Biso mean--26.7 36.53 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142314
X-RAY DIFFRACTIONf_angle_d1.5023122
X-RAY DIFFRACTIONf_chiral_restr0.075317
X-RAY DIFFRACTIONf_plane_restr0.008426
X-RAY DIFFRACTIONf_dihedral_angle_d14.77827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.68470.32681280.29381151127991
2.6847-2.78060.33941320.25641255138798
2.7806-2.89190.28291420.23612661408100
2.8919-3.02350.27011350.244912601395100
3.0235-3.18290.25871420.22512611403100
3.1829-3.38220.23481400.206112911431100
3.3822-3.64330.23181450.179612561401100
3.6433-4.00970.20341390.17212801419100
4.0097-4.58930.17121440.138912921436100
4.5893-5.77990.17761380.137312881426100
5.7799-43.45120.16831480.173113411489100

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