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- PDB-2a22: Structure of Vacuolar Protein Sorting 29 from Cryptosporidium Parvum -

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Basic information

Entry
Database: PDB / ID: 2a22
TitleStructure of Vacuolar Protein Sorting 29 from Cryptosporidium Parvum
Componentsvacuolar protein sorting 29
KeywordsPROTEIN TRANSPORT / VACUOLAR PROTEIN SORTING PROTEIN / ALPHA-BETA-BETA-ALPHA SANDWICH / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


retromer complex / retrograde transport, endosome to Golgi / protein transport / cytoplasmic vesicle / 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 speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsBrokx, S. / Zhao, Y. / Alam, Z. / Lew, J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. ...Brokx, S. / Zhao, Y. / Alam, Z. / Lew, J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: vacuolar protein sorting 29
B: vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)47,5542
Polymers47,5542
Non-polymers00
Water5,260292
1
A: vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.841, 78.841, 151.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe quaternary structure is a monomer

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Components

#1: Protein vacuolar protein sorting 29 / VESICLE PROTEIN SORTING 29 / VPS29


Mass: 23777.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5CYJ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.49 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% w/v PEG 400, 100 mM sodium citrate pH 5.6, 200 mM ammonium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.198→28.9 Å / Num. all: 24958 / Num. obs: 24958 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 22.89
Reflection shellResolution: 2.198→2.28 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.45 / Num. unique all: 2440 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W24

1w24


Resolution: 2.198→28.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.689 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21391 1267 5.1 %RANDOM
Rwork0.1679 ---
obs0.17024 23691 99.63 %-
all-24958 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.198→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 0 292 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223153
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9764281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17425.252139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7741511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022387
X-RAY DIFFRACTIONr_nbd_refined0.2120.21419
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22135
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.215
X-RAY DIFFRACTIONr_mcbond_it2.01632035
X-RAY DIFFRACTIONr_mcangle_it2.9843183
X-RAY DIFFRACTIONr_scbond_it4.18851292
X-RAY DIFFRACTIONr_scangle_it5.90171098
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 87 -
Rwork0.201 1716 -
obs--99.07 %

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