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- PDB-5bv1: Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bv1 | ||||||
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Title | Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum | ||||||
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![]() | TRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile | ||||||
Function / homology | ![]() CORVET complex / HOPS complex / vacuole fusion, non-autophagic / fungal-type vacuole / endosomal transport / ligase activity / vesicle-mediated transport / intracellular protein transport / actin binding / endosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Baker, R.W. / Jeffrey, P.D. / Hughson, F.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly. Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M. #1: ![]() Title: Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16* Authors: Baker, R.W. / Jeffrey, P.D. / Hughson, F.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 363 KB | Display | ![]() |
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PDB format | ![]() | 290.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.8 KB | Display | ![]() |
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Full document | ![]() | 509.3 KB | Display | |
Data in XML | ![]() | 60.6 KB | Display | |
Data in CIF | ![]() | 82.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5buzC ![]() 5bv0C ![]() 4kmoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA
NCS ensembles :
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Components
#1: Protein | Mass: 73990.117 Da / Num. of mol.: 2 / Fragment: unp residues 139-806 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: ![]() ![]() #2: Protein | Mass: 37912.211 Da / Num. of mol.: 2 / Fragment: unp residues 503-816 / Mutation: L672V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | Sequence details | Authors have indicated that the sequence for the UNProt entries G0S6M7_CHATD and G0SCM5_CHATD are not correct | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014 | |||||||||||||||||||||
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.902→159.902 Å / Num. obs: 53085 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 65.34 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.9 / Num. measured all: 300496 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KMO Resolution: 2.902→61.592 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.73 Å2 / Biso mean: 66.5912 Å2 / Biso min: 20.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.902→61.592 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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