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- PDB-4hl4: Crystal structure of the human TBC1D20 RabGAP domain -

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Basic information

Entry
Database: PDB / ID: 4hl4
TitleCrystal structure of the human TBC1D20 RabGAP domain
ComponentsTBC1 domain family member 20
KeywordsHYDROLASE ACTIVATOR / Tbc / RabGAP / Rab1b / Catalytic Domain / Fluorides / GTPase-Activating Proteins / Rab GTP-Binding Protein / GTP Hydrolase
Function / homology
Function and homology information


acrosome assembly / positive regulation of ER to Golgi vesicle-mediated transport / positive regulation by host of viral genome replication / COPII-coated vesicle cargo loading / lens fiber cell morphogenesis / positive regulation by virus of viral protein levels in host cell / lipid droplet organization / TBC/RABGAPs / COPII-mediated vesicle transport / virion assembly ...acrosome assembly / positive regulation of ER to Golgi vesicle-mediated transport / positive regulation by host of viral genome replication / COPII-coated vesicle cargo loading / lens fiber cell morphogenesis / positive regulation by virus of viral protein levels in host cell / lipid droplet organization / TBC/RABGAPs / COPII-mediated vesicle transport / virion assembly / seminiferous tubule development / Golgi organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / small GTPase binding / positive regulation of GTPase activity / nuclear membrane / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1310 / GTPase-activating protein TBC20/Gyp8-like / Ypt/Rab-GAP domain of gyp1p, domain 3 / 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. / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 ...Helicase, Ruva Protein; domain 3 - #1310 / GTPase-activating protein TBC20/Gyp8-like / Ypt/Rab-GAP domain of gyp1p, domain 3 / 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. / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / BERYLLIUM TRIFLUORIDE ION / TBC1 domain family member 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGazdag, E.M. / Gavriljuk, K. / Itzen, A. / Koetting, C. / Gerwert, K. / Goody, R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail.
Authors: Gavriljuk, K. / Gazdag, E.M. / Itzen, A. / Kotting, C. / Goody, R.S. / Gerwert, K.
History
DepositionOct 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TBC1 domain family member 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8744
Polymers33,6901
Non-polymers1843
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 73.550, 113.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TBC1 domain family member 20


Mass: 33689.727 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D20, C20orf140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96BZ9
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate pH 4.5, 0.8M di-potassium hydrogen phospate, 0.8M sodium dihydrogen phosphate, 0.025M beryllium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9793
SYNCHROTRONSLS X10SA20.9786
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELOct 9, 2011
PSI PILATUS 6M2PIXELOct 30, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) CHANNELSINGLE WAVELENGTHMx-ray1
2Si(111) CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97861
ReflectionResolution: 2.2→50 Å / Num. all: 18695 / Num. obs: 18508 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SOLVEphasing
REFMAC5.5.0102refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.531 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.237 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23489 926 5 %RANDOM
Rwork0.20259 ---
obs0.20425 17582 100 %-
all-18508 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.211 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å21.67 Å20 Å2
2--3.34 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 12 45 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222301
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9713138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73223.868106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94815375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.611514
X-RAY DIFFRACTIONr_chiral_restr0.1230.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211759
X-RAY DIFFRACTIONr_mcbond_it1.1421.51421
X-RAY DIFFRACTIONr_mcangle_it2.03222294
X-RAY DIFFRACTIONr_scbond_it3.1443880
X-RAY DIFFRACTIONr_scangle_it4.8834.5841
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 66 -
Rwork0.215 1255 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -30.3498 Å / Origin y: 1.5934 Å / Origin z: 17.7047 Å
111213212223313233
T0.1237 Å20.1277 Å20.0218 Å2-0.1859 Å20.026 Å2--0.192 Å2
L0.7603 °20.0964 °2-0.1423 °2-2.395 °2-0.5405 °2--3.6174 °2
S0.075 Å °0.1339 Å °0.0046 Å °-0.3063 Å °-0.1935 Å °-0.1852 Å °-0.0007 Å °0.3398 Å °0.1185 Å °

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