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- PDB-3vu4: Crystal structure of Kluyvelomyces marxianus Hsv2 -

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Basic information

Entry
Database: PDB / ID: 3vu4
TitleCrystal structure of Kluyvelomyces marxianus Hsv2
ComponentsKmHsv2
KeywordsPROTEIN TRANSPORT / beta-propeller fold
Function / homology: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / cytoplasm / KmHsv2
Function and homology information
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWatanabe, Y. / Noda, N.N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18.
Authors: Watanabe, Y. / Kobayashi, T. / Yamamoto, H. / Hoshida, H. / Akada, R. / Inagaki, F. / Ohsumi, Y. / Noda, N.N.
History
DepositionJun 15, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: KmHsv2
B: KmHsv2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,15515
Polymers81,9062
Non-polymers1,24913
Water2,486138
1
A: KmHsv2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7229
Polymers40,9531
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KmHsv2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4336
Polymers40,9531
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-177 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.270, 140.270, 251.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein KmHsv2


Mass: 40953.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: J3QW34*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUES (-4)-0 (GPLGS) ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUES (-4)-0 (GPLGS) ARE EXPRESSION TAGS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.3671.76
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M AcOH, 1.2M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2902
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A20.97918, 0.97932, 0.96409
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 12, 2012
ADSC QUANTUM 2102CCDMay 12, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979181
30.979321
40.964091
ReflectionResolution: 2.6→50 Å / Num. all: 45716 / Num. obs: 45676 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.4
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.556 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→39.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 92997.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4356 10.1 %RANDOM
Rwork0.224 ---
all0.227 45610 --
obs0.224 43238 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9707 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 65 138 5234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 646 9.9 %
Rwork0.305 5878 -
obs-6524 87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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