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- PDB-3qwl: Crystal structure of human TBC1 domain family member 7 -

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Basic information

Entry
Database: PDB / ID: 3qwl
TitleCrystal structure of human TBC1 domain family member 7
ComponentsTBC1 domain family member 7
KeywordsHYDROLASE ACTIVATOR / Rab GTPase activation / structural genomics consortium / TBC domain / SGC
Function / homology
Function and homology information


TSC1-TSC2 complex / negative regulation of cilium assembly / response to growth factor / activation of GTPase activity / negative regulation of TOR signaling / TBC/RABGAPs / negative regulation of TORC1 signaling / cellular response to starvation / GTPase activator activity / ciliary basal body ...TSC1-TSC2 complex / negative regulation of cilium assembly / response to growth factor / activation of GTPase activity / negative regulation of TOR signaling / TBC/RABGAPs / negative regulation of TORC1 signaling / cellular response to starvation / GTPase activator activity / ciliary basal body / positive regulation of protein ubiquitination / small GTPase binding / positive regulation of GTPase activity / cytoplasmic vesicle / lysosomal membrane / cytosol
Similarity search - Function
Ypt/Rab-GAP domain of gyp1p, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 1 / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 3 / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Cyclin A; domain 1 ...Ypt/Rab-GAP domain of gyp1p, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 1 / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 3 / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsGuan, X. / Tempel, W. / Tong, Y. / Wernimont, A.K. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human TBC1 domain family member 7
Authors: Guan, X. / Tempel, W. / Tong, Y. / Wernimont, A.K. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TBC1 domain family member 7


Theoretical massNumber of molelcules
Total (without water)34,0775
Polymers34,0771
Non-polymers04
Water79344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.574, 83.984, 87.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TBC1 domain family member 7


Mass: 34076.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D7, HSPC239, TBC7 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9P0N9
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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 (%)
11.8734.15
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, sitting drop8.520% PEG-1500, 0.2M magnesium chloride, 0.1M TRIS. 1:10 dispase-1 added in situ., pH 8.5, vapor diffusion, sitting drop, temperature 289K
2892vapor diffusion, sitting drop7.5Selenomethionyl derivative protein. 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES. 1:10 dispase-1 added in situ., pH 7.5, vapor diffusion, sitting drop, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97929
SYNCHROTRONAPS 19-ID20.97931
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 10, 2011
ADSC QUANTUM 3152CCDFeb 24, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979311
ReflectionResolution: 1.9→40 Å / Num. obs: 21049 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Χ2: 1.676 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.977.10.85520720.9521,2100
1.97-2.057.10.62720680.8661,2100
2.05-2.147.20.38320620.9221,2100
2.14-2.257.10.2620781.2161,2100
2.25-2.397.10.18120751.2411,2100
2.39-2.587.10.1220821.3231,2100
2.58-2.847.10.08621211.5811,2100
2.84-3.256.90.06821232.381,2100
3.25-4.096.60.05421343.5111,299.9
4.09-406.20.0422342.9891,297.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.365 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. SHELX and DM, RESOLVE were also used during structure solution and phase improvement. The program COOT and the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. SHELX and DM, RESOLVE were also used during structure solution and phase improvement. The program COOT and the molprobity server were used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1062 5.127 %RANDOM
Rwork0.2112 ---
obs0.213 20715 99.348 %-
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 max: 66.37 Å2 / Biso mean: 31.721 Å2 / Biso min: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.907 Å20 Å20 Å2
2---1.934 Å20 Å2
3---1.027 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 4 44 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222204
X-RAY DIFFRACTIONr_bond_other_d0.0010.021492
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9733001
X-RAY DIFFRACTIONr_angle_other_deg0.9233663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25923.57184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4691510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_mcbond_it0.681.51377
X-RAY DIFFRACTIONr_mcbond_other0.1711.5537
X-RAY DIFFRACTIONr_mcangle_it1.29822235
X-RAY DIFFRACTIONr_scbond_it2.1613827
X-RAY DIFFRACTIONr_scangle_it3.4914.5763
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 (%)
1.9-1.9490.393940.3461417151699.67
1.949-2.0020.309810.2731381147099.456
2.002-2.060.288730.2541346142599.579
2.06-2.1230.289700.241301137699.637
2.123-2.1920.306710.2321293137399.344
2.192-2.2690.311770.2651214130299.155
2.269-2.3540.334530.2421190125099.44
2.354-2.450.309610.2151162122699.755
2.45-2.5580.301680.2151094116899.486
2.558-2.6820.27650.221070114199.474
2.682-2.8250.269490.2411010106299.718
2.825-2.9950.239480.221962101599.507
2.995-3.20.323470.21693097899.898
3.2-3.4530.229370.22285589599.665
3.453-3.7770.253360.187805841100
3.777-4.2150.224350.16172276299.344
4.215-4.8510.154370.1664468299.853
4.851-5.9030.322240.20856659199.831
5.903-8.1910.239240.21944747299.788
8.191-300.186120.2124430683.66
Refinement TLS params.Method: refined / Origin x: 16.4736 Å / Origin y: 3.7006 Å / Origin z: 65.283 Å
111213212223313233
T0.0119 Å2-0.0107 Å2-0.0221 Å2-0.0669 Å2-0.0039 Å2--0.1125 Å2
L0.5844 °2-0.293 °2-0.1598 °2-2.0509 °2-0.4045 °2--2.0571 °2
S-0.0176 Å °-0.0151 Å °0.0775 Å °0.0562 Å °-0.0176 Å °-0.1355 Å °-0.0712 Å °-0.0684 Å °0.0352 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 292
2X-RAY DIFFRACTION1A298 - 341

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