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- PDB-2a70: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -

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Basic information

Entry
Database: PDB / ID: 2a70
TitleCrystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 2
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 / fungal-type vacuole membrane / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / 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: 1.1 Å
AuthorsSatoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Katoh, 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 ...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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Category: atom_site / Item: _atom_site.occupancy
Revision 2.1Oct 23, 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: Emp47p
B: Emp47p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0118
Polymers49,6392
Non-polymers3726
Water11,584643
1
A: Emp47p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0064
Polymers24,8191
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Emp47p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0064
Polymers24,8191
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.620, 65.210, 72.460
Angle α, β, γ (deg.)90.00, 96.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Emp47p


Mass: 24819.447 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG3350, Potassium acetate, pH 7.8, 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 16, 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: 1.05→50 Å / Num. all: 178928 / Num. obs: 176286 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.9
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Num. unique all: 15231 / % possible all: 85.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A6Z

2a6z


Resolution: 1.1→10 Å / Num. parameters: 37983 / Num. restraintsaints: 45315 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.173 7802 5.3 %RANDOM
Rwork0.135 ---
obs0.135 147540 95 %-
all-147540 --
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4165
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 24 643 4220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0315
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.091

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