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- PDB-3rru: X-ray crystal structure of the VHS domain of human TOM1-like prot... -

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Basic information

Entry
Database: PDB / ID: 3rru
TitleX-ray crystal structure of the VHS domain of human TOM1-like protein, Northeast Structural Genomics Consortium Target HR3050E
ComponentsTOM1L1 protein
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / super-helical protein / Src-activating and signaling molecule protein / Target of Myb-like protein 1
Function / homology
Function and homology information


Golgi stack / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / negative regulation of mitotic nuclear division / clathrin binding / activation of protein kinase activity / protein kinase activator activity / positive regulation of protein autophosphorylation / ubiquitin binding / intracellular protein transport / SH3 domain binding ...Golgi stack / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / negative regulation of mitotic nuclear division / clathrin binding / activation of protein kinase activity / protein kinase activator activity / positive regulation of protein autophosphorylation / ubiquitin binding / intracellular protein transport / SH3 domain binding / lysosome / endosome membrane / endosome / protein kinase binding / signal transduction / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
TOM1-like protein 1 / Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...TOM1-like protein 1 / Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
TOM1-like protein 1 / TOM1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Patel, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Patel, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of the VHS domain of human TOM1-like protein, Northeast Structural Genomics Consortium Target HR3050E
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Patel, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOM1L1 protein
B: TOM1L1 protein


Theoretical massNumber of molelcules
Total (without water)34,9672
Polymers34,9672
Non-polymers00
Water0
1
A: TOM1L1 protein


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TOM1L1 protein


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.047, 122.047, 55.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein TOM1L1 protein / Target of myb1-like 1 (Chicken) / isoform CRA_a


Mass: 17483.631 Da / Num. of mol.: 2 / Fragment: VHS_Tom1, residues 9-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_32771, tom1-like, TOM1L1 / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8N749, UniProt: O75674*PLUS

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 291 K / pH: 6
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 0.02% NaN3. Reservoir solution: 100mM MES (pH 6), 40% PEG 8000, and 100mM Ammonium Sulfate, micro batch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97916 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 28, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 18360 / Num. obs: 17498 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.104 / Net I/σ(I): 6.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 1.61 / Num. unique all: 1371 / Rsym value: 0.293 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SnBthen SOLVE/RESOLVEphasing
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 59077.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1634 9.3 %RANDOM
Rwork0.227 ---
all0.23 18360 --
obs0.227 17498 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 4.55384 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.76 Å20 Å20 Å2
2--4.76 Å20 Å2
3----9.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 0 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 138 9.1 %
Rwork0.368 1371 -
obs-1371 81.5 %

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