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- PDB-6xjl: Structure of the SM protein Vps45 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6xjl
TitleStructure of the SM protein Vps45
ComponentsVps45
KeywordsTRANSPORT PROTEIN / MEMBRANE TRAFFICKING / SM PROTEIN / THERMOPHILE
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport / Golgi membrane
Similarity search - Function
Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family
Similarity search - Domain/homology
Putative vacuolar protein sorting-associated protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJeffrey, P.D. / Shimamura, G.S. / Allen, F. / Hughson, F.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007388 United States
CitationJournal: Elife / Year: 2020
Title: The Sec1/Munc18 protein Vps45 holds the Qa-SNARE Tlg2 in an open conformation.
Authors: Eisemann, T.J. / Allen, F. / Lau, K. / Shimamura, G.R. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vps45


Theoretical massNumber of molelcules
Total (without water)71,6251
Polymers71,6251
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.489, 93.956, 102.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Vps45 / Putative vacuolar protein sorting-associated protein


Mass: 71625.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Rosetta / References: UniProt: G0S539
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 0.1 M sodium acetate pH 6.0, 3% (w/v) polyglycolide, 5% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 45356 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.042 / Rrim(I) all: 0.092 / Χ2: 1.098 / Net I/σ(I): 6.1 / Num. measured all: 209783
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.20.70822110.7430.3830.8071.10198.9
2.03-2.074.50.65422160.7810.3430.7411.17899.1
2.07-2.114.50.54122020.8210.2850.6131.11998.9
2.11-2.154.90.47922490.8910.2380.5361.11199.1
2.15-2.24.90.42322160.8990.2110.4741.16199.2
2.2-2.254.80.36322410.9280.1830.4071.1699.4
2.25-2.314.80.31922370.9390.1610.3581.13299.5
2.31-2.374.80.27422490.9550.1390.3081.12799.6
2.37-2.444.70.23122570.9610.1180.261.13299.5
2.44-2.524.50.18722430.9710.0980.2121.12599.8
2.52-2.614.30.15722400.9760.0850.1791.12399.6
2.61-2.714.50.14922690.9810.0780.1691.14999.7
2.71-2.844.90.12622650.9880.0630.1411.13199.8
2.84-2.994.90.10522780.9920.0520.1181.14899.8
2.99-3.174.80.0822630.9950.040.091.06199.9
3.17-3.424.70.0623060.9970.0310.0671.07799.9
3.42-3.764.30.04922940.9970.0260.0561.09199.9
3.76-4.314.50.04123140.9980.0220.0471.01199.9
4.31-5.424.80.03723320.9980.0180.0410.9299.9
5.42-354.30.03524740.9980.0190.040.91299.6

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→34.65 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2268 5.01 %
Rwork0.1794 43025 -
obs0.1814 45293 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.18 Å2 / Biso mean: 41.2475 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 2→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 270 4474
Biso mean---42.95 -
Num. residues----536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.040.29711380.26152572271097
2.04-2.090.28451430.23672635277899
2.09-2.140.26191320.21112660279299
2.14-2.20.27881310.2022645277699
2.2-2.260.23221550.19262630278599
2.26-2.340.21671490.18926682817100
2.34-2.420.24841310.18832674280599
2.42-2.520.24211460.179326782824100
2.52-2.630.24771360.181226962832100
2.63-2.770.22931320.180526782810100
2.77-2.940.25511550.186526752830100
2.94-3.170.24371260.189427212847100
3.17-3.490.21571400.174527292869100
3.49-3.990.20511550.154227232878100
4-5.030.17661450.146127572902100
5.03-34.650.19691540.193128843038100
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)
11.28861.0112-0.28782.5083-0.73451.1440.1885-0.2190.0160.3167-0.2250.0924-0.20120.09960.02410.257-0.02490.0020.233-0.00980.1567.09942.563839.6044
21.34430.0962-0.23343.0073-0.30032.0631-0.03560.0263-0.2436-0.1365-0.06430.00010.3761-0.07640.07880.2710.01670.04450.2487-0.03620.21889.05920.83838.0233
32.2163-0.77990.74732.4679-0.83062.10240.03370.16990.06180.0298-0.2122-0.3927-0.06990.46460.13250.2039-0.03080.02870.29430.06850.194418.804211.43720.1741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 235 )A-3 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 489 )A236 - 489
3X-RAY DIFFRACTION3chain 'A' and (resid 490 through 609 )A490 - 609

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