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- PDB-4v16: KlHsv2 with loop 6CD replaced by a Gly-Ser linker -

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Basic information

Entry
Database: PDB / ID: 4v16
TitleKlHsv2 with loop 6CD replaced by a Gly-Ser linker
ComponentsSVP1-LIKE PROTEIN 2
KeywordsPROTEIN TRANSPORT / PROPPIN / PHOSPHOINOSITIDE BINDING
Function / homology
Function and homology information


nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / extrinsic component of membrane / autophagy of mitochondrion / cytoplasmic vesicle membrane / protein transport / cytosol
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesKLUYVEROMYCES LACTIS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBusse, R.A. / Scacioc, A. / Krick, R. / Perez-Lara, A. / Thumm, M. / Kuhnel, K.
CitationJournal: Biophys.J. / Year: 2015
Title: Characterization of Proppin-Phosphoinositide Binding and Role of Loop 6Cd in Proppin-Membrane Binding.
Authors: Busse, R.A. / Scacioc, A. / Krick, R. / Perez-Lara, A. / Thumm, M. / Kuhnel, K.
History
DepositionSep 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SVP1-LIKE PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)37,5641
Polymers37,5641
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.700, 101.700, 78.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SVP1-LIKE PROTEIN 2 / HSV2


Mass: 37563.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSGSGSGSG REPLACES RESIDUES 257-274 / Source: (gene. exp.) KLUYVEROMYCES LACTIS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6CN23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREISUDES 257-274 WERE REPLACED WITH A GSGSGSGSG LINKER

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 14 % PEG 3350, 0.2 M MGCL2, 0.1 M TRIS PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 11779 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 47.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AV9

4av9


Resolution: 2.8→42.602 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 588 5 %
Rwork0.1983 --
obs0.2004 11776 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→42.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 0 7 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032397
X-RAY DIFFRACTIONf_angle_d0.7573258
X-RAY DIFFRACTIONf_dihedral_angle_d12.602844
X-RAY DIFFRACTIONf_chiral_restr0.031373
X-RAY DIFFRACTIONf_plane_restr0.002414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08170.32091430.26832735X-RAY DIFFRACTION100
3.0817-3.52750.26371460.22482775X-RAY DIFFRACTION100
3.5275-4.44350.23631470.17792792X-RAY DIFFRACTION100
4.4435-42.60720.20131520.17892886X-RAY DIFFRACTION100

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