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- PDB-2a71: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -

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Basic information

Entry
Database: PDB / ID: 2a71
TitleCrystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form
ComponentsEmp47p
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 / carbohydrate derivative binding / COPII-coated ER to Golgi transport vesicle / fungal-type vacuole membrane / endoplasmic reticulum-Golgi intermediate compartment / D-mannose binding / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi membrane / endoplasmic reticulum membrane
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: 2.7 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

Downloads & links

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Assembly

Deposited unit
A: Emp47p
B: Emp47p
C: Emp47p
D: Emp47p


Theoretical massNumber of molelcules
Total (without water)99,2784
Polymers99,2784
Non-polymers00
Water3,675204
1
A: Emp47p


Theoretical massNumber of molelcules
Total (without water)24,8191
Polymers24,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Emp47p


Theoretical massNumber of molelcules
Total (without water)24,8191
Polymers24,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Emp47p


Theoretical massNumber of molelcules
Total (without water)24,8191
Polymers24,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Emp47p


Theoretical massNumber of molelcules
Total (without water)24,8191
Polymers24,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.590, 129.620, 170.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Emp47p


Mass: 24819.447 Da / Num. of mol.: 4 / Fragment: RESIDUES 7-227
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: 854516, UniProt: P43555*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 43.6 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, Ammonium acetate, Sodium cacodylate, Calcuim chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 25245 / Num. obs: 22129 / % possible obs: 87.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2242 / % possible all: 90.9

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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 2A6Z

2a6z


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 14.811 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1125 5.1 %RANDOM
Rwork0.198 ---
all0.201 20823 --
obs0.201 20823 87.8 %-
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: 31.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6878 0 0 204 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217026
X-RAY DIFFRACTIONr_bond_other_d0.0020.026035
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9419516
X-RAY DIFFRACTIONr_angle_other_deg0.826314148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545865
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_restr0.0760.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021421
X-RAY DIFFRACTIONr_nbd_refined0.2070.21284
X-RAY DIFFRACTIONr_nbd_other0.2260.26911
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.24163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.54301
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26526943
X-RAY DIFFRACTIONr_scbond_it1.26832725
X-RAY DIFFRACTIONr_scangle_it2.2284.52573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.7 Å / Num. reflection Rwork: 1537 / Total num. of bins used: 20

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