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- PDB-2a6w: Crystal structure of Emp46p carbohydrate recognition domain (CRD)... -

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Basic information

Entry
Database: PDB / ID: 2a6w
TitleCrystal structure of Emp46p carbohydrate recognition domain (CRD), metal-free form
ComponentsEmp46p
KeywordsSUGAR BINDING PROTEIN / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


RHOC GTPase cycle / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment / D-mannose binding / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Emp46/Emp47 / EMP46/EMP47, N-terminal 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSatoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Kato, R. / Nakano, A. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
Authors: Satoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Yamada, Y. / Igarashi, N. / Kato, R. / Nakano, A. / Wakatsuki, S.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Emp46p
B: Emp46p


Theoretical massNumber of molelcules
Total (without water)51,1862
Polymers51,1862
Non-polymers00
Water5,405300
1
A: Emp46p


Theoretical massNumber of molelcules
Total (without water)25,5931
Polymers25,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Emp46p


Theoretical massNumber of molelcules
Total (without water)25,5931
Polymers25,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.93, 55.78, 77.66
Angle α, β, γ (deg.)90.00, 107.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Emp46p


Mass: 25593.084 Da / Num. of mol.: 2 / Fragment: RESIDUES 6-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 6323109, UniProt: Q12396*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG1000, HEPES, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 45402 / Num. obs: 45303 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4 / Num. unique all: 4517 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A6V

2a6v


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.856 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2272 5 %RANDOM
Rwork0.21 ---
all0.211 42874 --
obs0.211 42874 99.8 %-
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: 27.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.29 Å2
2---0.55 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 0 300 3787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223562
X-RAY DIFFRACTIONr_bond_other_d0.0020.023205
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9694791
X-RAY DIFFRACTIONr_angle_other_deg1.06137514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285432
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_restr0.0870.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined0.1970.2555
X-RAY DIFFRACTIONr_nbd_other0.2410.23750
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9921.52149
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79723451
X-RAY DIFFRACTIONr_scbond_it2.01231413
X-RAY DIFFRACTIONr_scangle_it3.3074.51340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 1.75 Å / Num. reflection Rwork: 3127 / Total num. of bins used: 20

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