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- PDB-6d0s: RabGAP domain of human TBC1D22B -

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Basic information

Entry
Database: PDB / ID: 6d0s
TitleRabGAP domain of human TBC1D22B
ComponentsTBC1 domain family member 22B
KeywordsPROTEIN BINDING / Rab-GAP / GTPase activator / TBC1 / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


activation of GTPase activity / GTPase activator activity / 14-3-3 protein binding / intracellular protein transport
Similarity search - Function
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TBC1 domain family member 22B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTong, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: RabGAP domain of human TBC1D22B
Authors: Tong, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Park, H.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJun 6, 2018ID: 3DZX
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: TBC1 domain family member 22B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,86912
Polymers41,7721
Non-polymers9611
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.015, 78.015, 217.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein TBC1 domain family member 22B / TBC1D22B


Mass: 41772.457 Da / Num. of mol.: 1 / Fragment: RabGAP domain (UNP residues 178-505)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D22B, C6orf197 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NU19
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.3
Details: 1.4 M ammonium sulfate, 0.1 M Bis-Tris, 0.001 M DTT, 1:100 chymotrypsin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.96749 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96749 Å / Relative weight: 1
ReflectionResolution: 2.3→42.38 Å / Num. obs: 18331 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.679 % / Biso Wilson estimate: 60.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.065 / Χ2: 1.085 / Net I/σ(I): 32.7 / Num. measured all: 379060 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.3621.4821.1923.4727798130712940.8481.2299
2.36-2.4221.6030.9234.6827630127912790.9160.945100
2.42-2.4921.7070.8385.3527025124512450.9240.858100
2.49-2.5721.5250.667.0126175121612160.9640.675100
2.57-2.6621.5070.5438.1925550118811880.9710.556100
2.66-2.7521.2910.42711.2624187113611360.9810.438100
2.75-2.8521.4580.31813.9723818111011100.9920.326100
2.85-2.9721.5180.2318.7423067107210720.9950.235100
2.97-3.121.3910.16625.2222033103010300.9980.17100
3.1-3.2521.1730.11633.2121215100210020.9990.119100
3.25-3.4321.1210.0941.74196649319310.9990.092100
3.43-3.6420.2750.06554.251818789889710.06699.9
3.64-3.8919.2580.05361.71660086286210.054100
3.89-4.219.6010.04271.971556379479410.043100
4.2-4.619.5930.03877.531459774574510.039100
4.6-5.1419.3440.03479.691303867467410.035100
5.14-5.9419.1430.03577.181179261661610.036100
5.94-7.2718.2080.03377.99961452852810.034100
7.27-10.2917.4420.02785.54762243743710.028100
10.29-42.3814.1270.0376.0838852862750.9980.03196.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSCONV0.6.3data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFZ

2qfz


Resolution: 2.3→42.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflection
Rfree0.239 930 5.09 %
Rwork0.197 --
obs0.199 18259 99.9 %
Displacement parametersBiso max: 155.14 Å2 / Biso mean: 67.89 Å2 / Biso min: 40.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.2751 Å20 Å20 Å2
2---2.2751 Å20 Å2
3---4.5502 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.3→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 15 0 2267
Biso mean--71.47 --
Num. residues----286
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d759SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2314HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2668SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2314HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3145HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion17.89
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2 162 5.66 %
Rwork0.2 2698 -
all-2860 -
obs--99.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.45550.5991.64533.832-0.30661.78980.04140.0579-0.3878-0.0287-0.1483-0.06320.0824-0.12840.1069-0.0128-0.0057-0.0128-0.2275-0.0342-0.148556.781813.3856-8.1472
23.28761.72540.37623.4135-0.21892.4996-0.15240.05940.27270.028-0.0357-0.0254-0.26250.06740.1881-0.0249-0.0335-0.13-0.15350.0082-0.107467.323336.1229-3.0119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|183 - A|363 }A183 - 363
2X-RAY DIFFRACTION2{ A|364 - A|500 }A364 - 500

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