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- PDB-2qfz: Crystal structure of human TBC1 domain family member 22A -

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Basic information

Entry
Database: PDB / ID: 2qfz
TitleCrystal structure of human TBC1 domain family member 22A
ComponentsTBC1 domain family member 22A
KeywordsHYDROLASE ACTIVATOR / RAB-GAP / gtpase activator / tbc1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


14-3-3 protein binding / GTPase activator activity / protein homodimerization activity
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 22A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsTong, Y. / Tempel, W. / Dimov, S. / Dong, A. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / Tempel, W. / Dimov, S. / Dong, A. / 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 human TBC1 domain family member 22A.
Authors: Tong, Y. / Tempel, W. / Dimov, S. / Dong, A. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,01714
Polymers82,0172
Non-polymers012
Water1,44180
1
A: TBC1 domain family member 22A


Theoretical massNumber of molelcules
Total (without water)41,0098
Polymers41,0091
Non-polymers07
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TBC1 domain family member 22A


Theoretical massNumber of molelcules
Total (without water)41,0096
Polymers41,0091
Non-polymers05
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.911, 121.515, 66.278
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number4
Space group name H-MP1211
Detailsnot known

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Components

#1: Protein TBC1 domain family member 22A


Mass: 41008.684 Da / Num. of mol.: 2 / Fragment: Rab-GAP TBC domain: Residues 191-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D22A, C22orf4 / Plasmid: pET28a-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8WUA7
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.5 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 28.0% PEG400, 0.2M Calcium chloride, 0.1M Sodium HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 39313 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.152 / Χ2: 1.934 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2.1-2.181006.10.96639351.131
2.18-2.261006.50.70139231.107
2.26-2.371006.50.53539071.136
2.37-2.491006.50.41339121.209
2.49-2.651006.60.3139381.258
2.65-2.851006.60.23339221.546
2.85-3.141006.60.17239081.992
3.14-3.591006.50.12439392.794
3.59-4.521006.40.09639323.754
4.52-3099.96.20.07439973.438

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.43 Å
Translation2.5 Å29.43 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G77

2g77


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.19 / SU B: 5.236 / SU ML: 0.143 / ESU R: 0.234 / ESU R Free: 0.202
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. arp/warp, molprobity, coot programs have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 2049 5.229 %thin shells
Rwork0.2021 ---
all0.205 ---
obs-39184 99.187 %-
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: 25.763 Å2
Baniso -1Baniso -2Baniso -3
1-0.597 Å20 Å2-1.056 Å2
2---0.924 Å20 Å2
3---0.193 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 12 80 4992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225041
X-RAY DIFFRACTIONr_bond_other_d0.0010.023441
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9476861
X-RAY DIFFRACTIONr_angle_other_deg0.99338324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67322.827237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8291538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021103
X-RAY DIFFRACTIONr_nbd_refined0.2060.21068
X-RAY DIFFRACTIONr_nbd_other0.1850.23261
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22453
X-RAY DIFFRACTIONr_nbtor_other0.0870.22353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.25
X-RAY DIFFRACTIONr_mcbond_it2.74223133
X-RAY DIFFRACTIONr_mcbond_other0.7721187
X-RAY DIFFRACTIONr_mcangle_it3.88334889
X-RAY DIFFRACTIONr_scbond_it2.77622251
X-RAY DIFFRACTIONr_scangle_it3.78631967
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.1-2.15400.24426830.244293291.507
2.154-2.2130.2962660.2225360.228281299.644
2.213-2.27700.22627520.226276399.602
2.277-2.3470.2662400.20923960.214264599.66
2.347-2.4230.282250.20723520.213258499.729
2.423-2.50800.2125110.21251699.801
2.508-2.6010.3091770.20822360.215241699.876
2.601-2.7070.2451530.21921980.221235999.661
2.707-2.82600.20522130.205221699.865
2.826-2.9630.2771630.21119540.216211999.906
2.963-3.1210.2521540.21218950.215205099.951
3.121-3.3090.2781250.20518310.209195899.898
3.309-3.5340.2891090.1916830.1971792100
3.534-3.8130.277920.18415990.189169299.941
3.813-4.170.164750.17214800.171155999.743
4.17-4.6510.186700.16613420.1671412100
4.651-5.3490.188480.17612170.1761265100
5.349-6.50.371830.2589770.266106199.906
6.5-8.9830.21360.2368050.23484299.881
8.983-300.246330.214750.21251299.219

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