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- PDB-4zy8: K. lactis Lst4 longin domain -

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Basic information

Entry
Database: PDB / ID: 4zy8
TitleK. lactis Lst4 longin domain
ComponentsProtein LST4
KeywordsTRANSPORT PROTEIN / longin / DENN
Function / homology
Function and homology information


FNIP-folliculin RagC/D GAP / amino acid transport / vacuolar membrane / positive regulation of TORC1 signaling / GTPase activator activity / protein transport
Similarity search - Function
Yeast longin domain / Yeast longin domain / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile.
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsPacitto, A. / Ascher, D.B. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Myrovlytis Trust United Kingdom
CitationJournal: Open Biology / Year: 2015
Title: Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein.
Authors: Pacitto, A. / Ascher, D.B. / Wong, L.H. / Blaszczyk, B.K. / Nookala, R.K. / Zhang, N. / Dokudovskaya, S. / Levine, T.P. / Blundell, T.L.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 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
C: Protein LST4
A: Protein LST4
B: Protein LST4
D: Protein LST4


Theoretical massNumber of molelcules
Total (without water)82,5624
Polymers82,5624
Non-polymers00
Water3,171176
1
C: Protein LST4


Theoretical massNumber of molelcules
Total (without water)20,6411
Polymers20,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Protein LST4


Theoretical massNumber of molelcules
Total (without water)20,6411
Polymers20,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protein LST4


Theoretical massNumber of molelcules
Total (without water)20,6411
Polymers20,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein LST4


Theoretical massNumber of molelcules
Total (without water)20,6411
Polymers20,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.703, 120.703, 93.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Protein LST4


Mass: 20640.516 Da / Num. of mol.: 4 / Fragment: UNP residues 58-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: LST4, KLLA0A06622g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CXP4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: Sodium chloride, Butan-1-ol, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→35.29 Å / Num. obs: 38603 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.4
Reflection shellResolution: 2.14→2.216 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→35.29 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1860 4.83 %
Rwork0.2106 --
obs0.2126 38544 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 0 176 4584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134511
X-RAY DIFFRACTIONf_angle_d1.36152
X-RAY DIFFRACTIONf_dihedral_angle_d11.7151533
X-RAY DIFFRACTIONf_chiral_restr0.073773
X-RAY DIFFRACTIONf_plane_restr0.008752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.19790.3251420.25972772X-RAY DIFFRACTION100
2.1979-2.26250.30371410.23852769X-RAY DIFFRACTION100
2.2625-2.33550.2481300.22692774X-RAY DIFFRACTION100
2.3355-2.4190.27081330.22992807X-RAY DIFFRACTION100
2.419-2.51580.29051420.22932779X-RAY DIFFRACTION100
2.5158-2.63030.28391480.23722796X-RAY DIFFRACTION100
2.6303-2.76890.24791440.24092776X-RAY DIFFRACTION100
2.7689-2.94230.3181460.24142812X-RAY DIFFRACTION100
2.9423-3.16940.28941470.23222807X-RAY DIFFRACTION100
3.1694-3.48810.25081500.20752813X-RAY DIFFRACTION100
3.4881-3.99220.2591480.19552841X-RAY DIFFRACTION100
3.9922-5.02740.20121380.16812905X-RAY DIFFRACTION100
5.0274-35.29730.22761510.21423033X-RAY DIFFRACTION100

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