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- PDB-2dup: Crystal structure of VIP36 exoplasmic/lumenal domain, metal-free form -

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Basic information

Entry
Database: PDB / ID: 2dup
TitleCrystal structure of VIP36 exoplasmic/lumenal domain, metal-free form
ComponentsVesicular integral-membrane protein VIP36
KeywordsPROTEIN TRANSPORT / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum-Golgi intermediate compartment / D-mannose binding / heat shock protein binding / positive regulation of phagocytosis / protein transport ...COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum-Golgi intermediate compartment / D-mannose binding / heat shock protein binding / positive regulation of phagocytosis / protein transport / cytoplasmic vesicle / Golgi membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
VIP36, lectin domain / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vesicular integral-membrane protein VIP36
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSatoh, T. / Cowieson, N.P. / Kato, R. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
Authors: Satoh, T. / Cowieson, N.P. / Hakamata, W. / Ideo, H. / Fukushima, K. / Kurihara, M. / Kato, R. / Yamashita, K. / Wakatsuki, S.
History
DepositionJul 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicular integral-membrane protein VIP36
B: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,32110
Polymers57,8632
Non-polymers4588
Water3,495194
1
A: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2266
Polymers28,9311
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0944
Polymers28,9311
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.000, 45.200, 117.100
Angle α, β, γ (deg.)90.00, 132.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vesicular integral-membrane protein VIP36 / Lectin / mannose-binding 2 / VIP36


Mass: 28931.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 51-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: LMAN2 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49256
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop, soaking / pH: 6.5
Details: Crystallization: 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, SOAKING, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 38945 / Num. obs: 36474 / % possible obs: 93.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3041 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DUO

2duo


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.602 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1828 5 %RANDOM
Rwork0.225 ---
all0.228 34622 --
obs0.228 34622 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å23.4 Å2
2---0.29 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 23 194 4130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214039
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9315468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86223.45200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91315665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5691526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023100
X-RAY DIFFRACTIONr_nbd_refined0.1930.21556
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2255
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.210
X-RAY DIFFRACTIONr_mcbond_it0.9121.52462
X-RAY DIFFRACTIONr_mcangle_it1.50323872
X-RAY DIFFRACTIONr_scbond_it1.7431828
X-RAY DIFFRACTIONr_scangle_it2.5714.51596
LS refinement shellHighest resolution: 2.1 Å / Num. reflection Rwork: 2085 / Total num. of bins used: 20

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