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- PDB-2qq8: Crystal structure of the putative RabGAP domain of human TBC1 dom... -

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Basic information

Entry
Database: PDB / ID: 2qq8
TitleCrystal structure of the putative RabGAP domain of human TBC1 domain family member 14
ComponentsTBC1 domain family member 14
KeywordsHYDROLASE ACTIVATOR / Structural Genomics Consortium / Rab-GAP / TBC1D14 / SGC / GTPase activation
Function / homology
Function and homology information


recycling endosome to Golgi transport / small GTPase binding => GO:0031267 / regulation of autophagosome assembly / activation of GTPase activity / TBC/RABGAPs / autophagosome / negative regulation of autophagy / GTPase activator activity / intracellular protein transport / recycling endosome ...recycling endosome to Golgi transport / small GTPase binding => GO:0031267 / regulation of autophagosome assembly / activation of GTPase activity / TBC/RABGAPs / autophagosome / negative regulation of autophagy / GTPase activator activity / intracellular protein transport / recycling endosome / autophagy / intracellular membrane-bounded organelle / protein kinase binding / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / 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 ...Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / 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 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TBC1 domain family member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2 Å
AuthorsTong, Y. / Tempel, W. / Dimov, S. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the putative RabGAP domain of human TBC1 domain family member 14.
Authors: Tong, Y. / Tempel, W. / Dimov, S. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TBC1 domain family member 14


Theoretical massNumber of molelcules
Total (without water)38,6414
Polymers38,6411
Non-polymers03
Water1,62190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.520, 123.520, 48.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-30-

HOH

Detailsnot known

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Components

#1: Protein TBC1 domain family member 14


Mass: 38641.297 Da / Num. of mol.: 1 / Fragment: Putative RabGAP domain: Residues 357-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D14, KIAA1322 / Plasmid: pET28a-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9P2M4
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.448.73
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion7.525% PEG 4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 291K
2912vapor diffusion6.52.0M Sodium chloride, 0.1M Sodium dihydrogen phosphate, 0.1M MES, 0.1M Potassium dihydrogen phosphate, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.9177
SYNCHROTRONAPS 19-ID20.97937
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDApr 12, 2007
ADSC QUANTUM 2702CCDApr 12, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91771
20.979371
ReflectionResolution: 2→40 Å / Num. obs: 48699 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.34 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0710.10.48848450.91299.9
2.07-2.1511.40.37148860.911100
2.15-2.2511.50.27948891.033100
2.25-2.3711.60.21748381.009100
2.37-2.5211.60.16748941.028100
2.52-2.7111.60.13148751.099100
2.71-2.9911.60.09848451.258100
2.99-3.4211.60.07548681.531100
3.42-4.3111.60.06348662.046100
4.31-4011.10.06548932.55100

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.3.0037refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.183 / SU B: 3.254 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/wARP, Coot, Molprobity programs have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1307 5.033 %RANDOM
Rwork0.195 ---
all0.197 ---
obs-25967 99.973 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.346 Å20 Å20 Å2
2--0.346 Å20 Å2
3----0.692 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 3 90 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222367
X-RAY DIFFRACTIONr_bond_other_d0.0010.021557
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9423232
X-RAY DIFFRACTIONr_angle_other_deg0.98333801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1585297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.43824.231104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.014158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined0.2150.2515
X-RAY DIFFRACTIONr_nbd_other0.1810.21505
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21191
X-RAY DIFFRACTIONr_nbtor_other0.0860.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it2.62921499
X-RAY DIFFRACTIONr_mcbond_other0.7632582
X-RAY DIFFRACTIONr_mcangle_it3.79532347
X-RAY DIFFRACTIONr_scbond_it2.61521015
X-RAY DIFFRACTIONr_scangle_it3.893880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0510.2961000.2131765186699.946
2.051-2.1070.213680.18817681836100
2.107-2.1670.251940.19416651759100
2.167-2.2330.237880.1916311719100
2.233-2.3060.258800.18516071687100
2.306-2.3850.189810.18115391620100
2.385-2.4740.196890.18514801569100
2.474-2.5730.259820.19714411523100
2.573-2.6860.227840.19513691453100
2.686-2.8140.233770.2113321409100
2.814-2.9630.265680.21312601328100
2.963-3.1390.259620.21511931255100
3.139-3.350.27580.21711481206100
3.35-3.610.261650.19310551120100
3.61-3.9410.219550.1839921047100
3.941-4.3850.157410.161918959100
4.385-5.0240.195420.151812854100
5.024-6.0580.298310.222720751100
6.058-8.1990.295210.253584605100
8.199-200.212210.19738140898.529

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