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- PDB-1s31: Crystal Structure Analysis of the human Tub protein (isoform a) s... -

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Basic information

Entry
Database: PDB / ID: 1s31
TitleCrystal Structure Analysis of the human Tub protein (isoform a) spanning residues 289 through 561
Componentstubby isoform a
KeywordsSIGNALING PROTEIN / BETA BARREL / HYDROPHOBIC HELIX / HYDROPHOBIC CORE
Function / homology
Function and homology information


intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / protein localization to cilium / photoreceptor cell maintenance / positive regulation of phagocytosis / response to hormone ...intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / protein localization to cilium / photoreceptor cell maintenance / positive regulation of phagocytosis / response to hormone / G protein-coupled receptor binding / sensory perception of sound / cilium / retina development in camera-type eye / protein-containing complex binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tubby Protein; Chain A / Tubby Protein; Chain A / Tubby, N-terminal / Tubby N-terminal / Tubby, C-terminal / Tubby, C-terminal, conserved site / Tub family / Tub family signature 1. / Tub family signature 2. / Tubby-like, C-terminal ...Tubby Protein; Chain A / Tubby Protein; Chain A / Tubby, N-terminal / Tubby N-terminal / Tubby, C-terminal / Tubby, C-terminal, conserved site / Tub family / Tub family signature 1. / Tub family signature 2. / Tubby-like, C-terminal / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Tubby protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.704 Å
AuthorsBoutboul, S. / Carroll, K.J. / Basdevant, A. / Gomez, C. / Nandrot, E. / Clement, K. / Shapiro, L. / Abitbol, M.
Citation
Journal: To be Published
Title: A novel human obesity and sensory deficit syndrome resulting from a mutation in the TUB gene
Authors: Boutboul, S. / Carroll, K.J. / Basdevant, A. / Gomez, C. / Nandrot, E. / Clement, K. / Shapiro, L. / Abitbol, M.
#1: Journal: METHODS ENZYMOL. / Year: 1997
Title: Processing of X-ray Diffraction Data Collected in Oscillation Mode
Authors: Otwinowski, Z. / Minor, W.
#2: Journal: ACTA CRYSTALLOGR.,SECT.A / Year: 1994
Title: AMoRe: an Automated Package for Molecular Replacement
Authors: Navaza, J.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1997
Title: Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Authors: Murshudov, G.N. / Vagin, A.A. / Dodson, E.J.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tubby isoform a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9482
Polymers30,7981
Non-polymers1501
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tubby isoform a
hetero molecules

A: tubby isoform a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8964
Polymers61,5962
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3120 Å2
ΔGint-11 kcal/mol
Surface area27120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.981, 149.981, 149.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein tubby isoform a


Mass: 30798.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tub / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P50607
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / 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

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 400, 5mM Magnesium Chloride, 100mM Sodium Acetate, 15mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K, pH 5.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9814 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 15560 / Num. obs: 15503 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 24 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 30.9
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 100 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 10.1 / Num. unique all: 1511 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.7 / Cor.coef. Fo:Fc: 72.5
Highest resolutionLowest resolution
Rotation4 Å8 Å
Translation4 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoRECCP4 4.2phasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C8Z

1c8z


Resolution: 2.704→18.474 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.137 / SU ML: 0.155 / SU R Cruickshank DPI: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.243 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 767 4.967 %Random
Rwork0.1814 ---
obs0.1836 14674 100 %-
all-14674 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.802 Å2
Refinement stepCycle: LAST / Resolution: 2.704→18.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 10 90 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONBond distances: refined atoms0.0170.0222189
X-RAY DIFFRACTIONBond distances: others0.0010.021976
X-RAY DIFFRACTIONBond angles : refined atoms1.6121.9442959
X-RAY DIFFRACTIONBond angles : others0.89934600
X-RAY DIFFRACTIONTorsion angles, period 1. refined7.7225271
X-RAY DIFFRACTIONTorsion angles, period 2. refined35.39523.922102
X-RAY DIFFRACTIONTorsion angles, period 3. refined20.36815373
X-RAY DIFFRACTIONTorsion angles, period 4. refined21.6361517
X-RAY DIFFRACTIONChiral centres: refined atoms0.0990.2326
X-RAY DIFFRACTIONPlanar groups: refined atoms0.0050.022434
X-RAY DIFFRACTIONPlanar groups: others0.0010.02441
X-RAY DIFFRACTIONVDW repulsions: refined atoms0.2260.2425
X-RAY DIFFRACTIONVDW repulsions: others0.20.21985
X-RAY DIFFRACTIONVDW; torsion: refined atoms0.1840.21089
X-RAY DIFFRACTIONVDW; torsion: others0.0950.21379
X-RAY DIFFRACTIONHBOND: refined atoms0.1460.295
X-RAY DIFFRACTIONVDW repulsions; symmetry: refined atoms0.2710.27
X-RAY DIFFRACTIONVDW repulsions; symmetry: others0.2820.228
X-RAY DIFFRACTIONHBOND; symmetry: refined atoms0.1210.26
X-RAY DIFFRACTIONM. chain bond B values: refined atoms1.081.51384
X-RAY DIFFRACTIONM. chain bond B values: others0.1381.5550
X-RAY DIFFRACTIONM. chain angle B values: refined atoms1.90322200
X-RAY DIFFRACTIONM. chain angle B values: others0.94821860
X-RAY DIFFRACTIONS. chain bond B values: refined atoms1.9523889
X-RAY DIFFRACTIONS. chain bond B values: others0.64131694
X-RAY DIFFRACTIONS. chain angle B values: refined atoms3.3614.5759
X-RAY DIFFRACTIONS. chain angle B values: others1.4684.52740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection all
2.704-2.77290.281720.2281033X-RAY DIFFRACTION1105
2.773-2.84710.32400.2131021X-RAY DIFFRACTION1061
2.847-2.92760.207570.2161016X-RAY DIFFRACTION1073
2.928-3.01540.232380.2151002X-RAY DIFFRACTION1040
3.015-3.11150.288470.192937X-RAY DIFFRACTION984
3.111-3.21740.253570.192912X-RAY DIFFRACTION969
3.217-3.3350.23430.189883X-RAY DIFFRACTION926
3.335-3.46650.219390.188862X-RAY DIFFRACTION901
3.466-3.61480.216430.184813X-RAY DIFFRACTION856
3.615-3.7840.279450.188786X-RAY DIFFRACTION831
3.784-3.97950.233370.183749X-RAY DIFFRACTION786
3.979-4.20870.181400.172723X-RAY DIFFRACTION763
4.209-4.48270.182480.145658X-RAY DIFFRACTION706
4.483-4.81820.237350.142636X-RAY DIFFRACTION671
4.818-5.24260.219200.159589X-RAY DIFFRACTION609
5.243-5.80330.246270.186542X-RAY DIFFRACTION569
5.803-6.59350.289200.211496X-RAY DIFFRACTION516
6.593-7.82980.264230.195418X-RAY DIFFRACTION441
7.83-10.19520.176230.156344X-RAY DIFFRACTION367
10.195-18.47420.149130.179254X-RAY DIFFRACTION267
Refinement TLS params.Method: refined / Origin x: 121.874 Å / Origin y: 21.189 Å / Origin z: 73.111 Å
111213212223313233
T0.0595 Å2-0.0229 Å2-0.0135 Å2-0.0593 Å2-0.0334 Å2--0.1429 Å2
L1.5789 °20.9031 °20.1422 °2-2.8262 °2-0.349 °2--0.7035 °2
S-0.0774 Å °-0.0139 Å °0.2364 Å °-0.0491 Å °0.1017 Å °0.3134 Å °-0.1653 Å °0.0078 Å °-0.0244 Å °
Refinement TLS groupSelection: ALL

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