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- PDB-5hiu: Structure of the TSC2 N-terminus -

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Basic information

Entry
Database: PDB / ID: 5hiu
TitleStructure of the TSC2 N-terminus
ComponentsGTPase activator-like protein
KeywordsSIGNALING PROTEIN / complex
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / GTPase activator activity / nucleus
Similarity search - Function
Tuberin-type domain / Tuberin, N-terminal / Tuberin/Ral GTPase-activating protein subunit alpha / Tuberin / Domain of unknown function (DUF3384) / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / Armadillo-type fold
Similarity search - Domain/homology
GTPase activator-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsZech, R. / Kiontke, S. / Kummel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKU 2531/2-1 Germany
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Structure of the Tuberous Sclerosis Complex 2 (TSC2) N Terminus Provides Insight into Complex Assembly and Tuberous Sclerosis Pathogenesis.
Authors: Zech, R. / Kiontke, S. / Mueller, U. / Oeckinghaus, A. / Kummel, D.
#1: Journal: To Be Published
Title: Structure of the TSC2 N-terminal domain provides insight into TSC complex assembly and tuberous sclerosis pathogenesis
Authors: Zech, R. / Kiontke, S. / Mueller, U. / Oeckinghaus, A. / Kummel, D.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase activator-like protein
B: GTPase activator-like protein
C: GTPase activator-like protein
D: GTPase activator-like protein


Theoretical massNumber of molelcules
Total (without water)206,1894
Polymers206,1894
Non-polymers00
Water1629
1
A: GTPase activator-like protein


Theoretical massNumber of molelcules
Total (without water)51,5471
Polymers51,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase activator-like protein


Theoretical massNumber of molelcules
Total (without water)51,5471
Polymers51,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase activator-like protein


Theoretical massNumber of molelcules
Total (without water)51,5471
Polymers51,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase activator-like protein


Theoretical massNumber of molelcules
Total (without water)51,5471
Polymers51,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.730, 78.100, 153.750
Angle α, β, γ (deg.)89.90, 89.85, 78.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 88 - 527 / Label seq-ID: 21 - 460

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22DD

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999994, 0.000949, 0.003322), (-0.000939, -0.999995, 0.003068), (0.003324, 0.003065, 0.99999)28.52246, 234.65594, 76.41638
3given(1), (1), (1)
4given(-0.999995, 0.001858, 0.002542), (-0.001853, -0.999997, 0.001865), (0.002546, 0.00186, 0.999995)43.33321, 311.39493, 76.52258

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Components

#1: Protein
GTPase activator-like protein / TSC2


Mass: 51547.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0061860 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM Tris (pH 7.0), 14 % PEG 6000, 15 % Glycerol, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.3→41.9 Å / Num. obs: 83768 / % possible obs: 96.6 % / Redundancy: 3.6 % / Rrim(I) all: 0.035 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementResolution: 2.5→41.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 36.566 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26323 3326 5.1 %RANDOM
Rwork0.22369 ---
obs0.22577 62038 96.79 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.644 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å23.32 Å20.53 Å2
2--3.82 Å2-0.31 Å2
3----5.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12803 0 0 9 12812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212883
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.96317711
X-RAY DIFFRACTIONr_angle_other_deg0.769329576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62951595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51423.972569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.364152303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4761581
X-RAY DIFFRACTIONr_chiral_restr0.0640.22083
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022948
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3055.0536446
X-RAY DIFFRACTIONr_mcbond_other3.3045.0526445
X-RAY DIFFRACTIONr_mcangle_it5.0027.5718019
X-RAY DIFFRACTIONr_mcangle_other5.0027.5718020
X-RAY DIFFRACTIONr_scbond_it3.435.4026614
X-RAY DIFFRACTIONr_scbond_other3.435.4036615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4367.9629693
X-RAY DIFFRACTIONr_long_range_B_refined7.73440.86215657
X-RAY DIFFRACTIONr_long_range_B_other7.73440.86415658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A64271.89
22C63551.82
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 241 -
Rwork0.347 4608 -
obs--97.45 %
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)
11.6816-1.37431.95772.3376-3.01678.3844-0.06090.06140.1104-0.13030.10450.16690.3486-0.4051-0.04360.0588-0.0458-0.00970.0440.01970.099414.0989106.365116.7125
21.6764-1.4228-2.00942.32733.05338.529-0.0240.0594-0.0905-0.15250.1051-0.1566-0.38770.4005-0.08110.1009-0.0477-0.03440.0434-0.02010.124914.623128.44839.703
32.0448-1.27881.53141.6121-1.94696.62970.30660.091-0.1854-0.05350.1294-0.09210.21580.0501-0.4360.2879-0.0026-0.09640.0826-0.08450.256911.914156.2743103.7538
42.0437-1.2793-1.58561.59731.91956.58410.32790.08720.1766-0.0570.12620.0808-0.2377-0.0716-0.45410.31550.01250.01450.08530.0780.257631.8859155.044926.7447
519.4561-22.82539.083627.0271-10.54124.3274-0.34320.07570.923-0.0305-0.0972-1.1202-0.37220.14710.44040.765-0.0259-0.00290.40720.05940.45-24.3855141.9665101.1729
618.9824-23.3535-3.071430.69954.61970.8571-0.6692-0.5094-0.59530.33090.21981.5584-0.0838-0.10190.44940.6215-0.0148-0.09980.426-0.06010.457253.256992.899723.8955
72.3583-7.68993.330925.5559-12.06229.6406-0.0431-0.1711-0.0020.08140.70040.3191-0.2967-0.3843-0.65730.0902-0.0394-0.06680.3243-0.00430.271141.8898113.4388121.0973
83.911-8.2874-4.733626.6977.86996.3439-0.3101-0.34340.37140.00571.1173-0.07280.48420.3898-0.80720.09880.01680.01470.3388-0.0490.45521.9284198.041744.1933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 463
2X-RAY DIFFRACTION1A489 - 527
3X-RAY DIFFRACTION2B88 - 463
4X-RAY DIFFRACTION2B489 - 527
5X-RAY DIFFRACTION3C88 - 466
6X-RAY DIFFRACTION3C484 - 527
7X-RAY DIFFRACTION4D88 - 466
8X-RAY DIFFRACTION4D484 - 527
9X-RAY DIFFRACTION5A477 - 482
10X-RAY DIFFRACTION6B476 - 482
11X-RAY DIFFRACTION7C475 - 483
12X-RAY DIFFRACTION8D475 - 483

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