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- PDB-6jl7: crystal structure of TBC1D23 N terminal domain -

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Basic information

Entry
Database: PDB / ID: 6jl7
Titlecrystal structure of TBC1D23 N terminal domain
ComponentsTBC1 domain family member 23
KeywordsPROTEIN TRANSPORT / Vesicle transport / bridging factor
Function / homology
Function and homology information


vesicle tethering to Golgi / embryonic brain development / retrograde transport, endosome to Golgi / vesicle-mediated transport / trans-Golgi network / brain development / neuron projection development / cytoplasmic vesicle / Golgi apparatus / cytosol
Similarity search - Function
TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Rhodanese-like domain / Rhodanese domain profile. ...TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
TBC1 domain family member 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSun, Q. / Hu, W. / Jia, D.
CitationJournal: Plos Biol. / Year: 2020
Title: Structure of TBC1D23 N-terminus reveals a novel role for rhodanese domain.
Authors: Liu, D. / Yang, F. / Liu, Z. / Wang, J. / Huang, W. / Meng, W. / Billadeau, D.D. / Sun, Q. / Mo, X. / Jia, D.
History
DepositionMar 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: 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 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TBC1 domain family member 23


Theoretical massNumber of molelcules
Total (without water)50,4881
Polymers50,4881
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.736, 151.736, 38.604
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 TBC1 domain family member 23 / HCV non-structural protein 4A-transactivated protein 1


Mass: 50487.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D23, NS4ATP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MES pH6.5, 0.5 M Ammonium nitrate, 25% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17980 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.051 / Rrim(I) all: 0.159 / Χ2: 0.859 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2Rmerge(I) obsRrim(I) all
2.5-2.54149030.4530.5370.677
2.54-2.5913.98740.3580.5010.672
2.59-2.6413.88710.510.4450.673
2.64-2.6913.99050.5410.4010.671
2.69-2.7513.58970.7020.3530.667
2.75-2.8212.58750.7780.3340.702
2.82-2.8914.18930.8120.270.6970.978
2.89-2.9614.59040.8480.2320.710.8540.885
2.96-3.0514.68650.9290.1740.7160.6440.668
3.05-3.1514.68950.9450.140.7650.5160.534
3.15-3.2614.39020.9650.1150.7980.4210.436
3.26-3.3913.88840.9820.0870.8810.3130.325
3.39-3.5513.69100.9860.0710.9830.2510.261
3.55-3.7314.98900.9890.0531.0760.1970.204
3.73-3.9714.98910.990.0451.0820.1690.175
3.97-4.2714.79010.9930.0381.0670.140.145
4.27-4.713.69160.9930.0361.0150.1280.133
4.7-5.3815.19060.9940.0331.0630.1250.13
5.38-6.7813.89260.9880.0371.0770.1320.137
6.78-5013.69720.9940.0311.0950.1110.115

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2524 / WRfactor Rwork: 0.2149 / FOM work R set: 0.739 / SU B: 14.237 / SU ML: 0.288 / SU R Cruickshank DPI: 0.656 / SU Rfree: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.656 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 955 5.3 %RANDOM
Rwork0.2173 ---
obs0.2191 16995 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.75 Å2 / Biso mean: 84.57 Å2 / Biso min: 43.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å2-0 Å2
3---2.65 Å2
Refinement stepCycle: final / Resolution: 2.5→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 0 82 3605
Biso mean---64.5 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0143602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173217
X-RAY DIFFRACTIONr_angle_refined_deg0.7421.654882
X-RAY DIFFRACTIONr_angle_other_deg0.6681.6617542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8425443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64424.293184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00915600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7191512
X-RAY DIFFRACTIONr_chiral_restr0.0360.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
LS refinement shellResolution: 2.503→2.568 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 73 -
Rwork0.366 1251 -
all-1324 -
obs--99.4 %

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