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- PDB-1w24: Crystal Structure Of human Vps29 -

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Basic information

Entry
Database: PDB / ID: 1w24
TitleCrystal Structure Of human Vps29
ComponentsVACUOLAR PROTEIN SORTING PROTEIN 29
KeywordsCYTOPLASMIC PROTEIN / VACUOLAR PROTEIN SORTING PROTEIN / ALPHA-BETA-BETA-ALPHA SANDWICH
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome / endosome membrane ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome / endosome membrane / intracellular membrane-bounded organelle / metal ion binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.1 Å
AuthorsWang, D. / Guo, M. / Teng, M. / Niu, L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Human Vacuolar Protein Sorting Protein 29 Reveals a Phosphodiesterase/Nuclease-Like Fold and Two Protein-Protein Interaction Sites.
Authors: Wang, D. / Guo, M. / Liang, Z. / Fan, J. / Zhu, Z. / Zang, J. / Zhu, Z. / Li, X. / Teng, M. / Niu, L. / Dong, Y. / Liu, P.
History
DepositionJun 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: VACUOLAR PROTEIN SORTING PROTEIN 29


Theoretical massNumber of molelcules
Total (without water)20,5321
Polymers20,5321
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.871, 53.871, 124.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein VACUOLAR PROTEIN SORTING PROTEIN 29 / VESICLE PROTEIN SORTING 29


Mass: 20531.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: POSSIBLE ROLE IN VESICULAR PROTEIN SORTING

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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: 2.19 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5
Details: 25%PEG4000, 10%ETHYENE GLYCOL, 100MM HEPES PH7.5, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %PEG40001reservoir
210 %ethylene glycol1reservoir
3100 mMHEPES1reservoirpH7.5
43 mg/mlprotein1drop
550 mM1dropNaCl
65 mMTris-HCl1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 10937 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. obs: 10686 / Redundancy: 4.97 % / Num. measured all: 54013 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
AUTOMARdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→14.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 573 5.3 %RANDOM
Rwork0.218 ---
obs0.219 10289 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 0 48 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9571971
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9055178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021082
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.3587
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.5120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.326
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6622893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.85431448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8062563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.883523
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.309 57
Rwork0.283 959
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.18

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