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Yorodumi- PDB-5bv1: Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bv1 | ||||||
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Title | Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile | ||||||
Function / homology | Function and homology information vacuole organization / ligase activity / endomembrane system / vesicle-mediated transport / intracellular protein transport / intracellular membrane-bounded organelle / protein-containing complex / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.902 Å | ||||||
Authors | Baker, R.W. / Jeffrey, P.D. / Hughson, F.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2015 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: Journal: Plos One / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bv1.cif.gz | 363 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bv1.ent.gz | 290.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/5bv1 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/5bv1 | HTTPS FTP |
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-Related structure data
Related structure data | 5buzC 5bv0C 4kmoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5 #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.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||
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: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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