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- PDB-2a6z: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -

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Basic information

Entry
Database: PDB / ID: 2a6z
TitleCrystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1
ComponentsEmp47p (form2)
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: 1 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 9, 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 (form2)


Theoretical massNumber of molelcules
Total (without water)24,8191
Polymers24,8191
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.52, 64.99, 41.54
Angle α, β, γ (deg.)90.00, 96.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-256-

HOH

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Components

#1: Protein Emp47p (form2)


Mass: 24819.447 Da / Num. of mol.: 1 / 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.: 320 / 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: 6.3
Details: PEG3350, Ammonium chloride, pH 6.3, 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: 1→50 Å / Num. all: 103133 / Num. obs: 99298 / % possible obs: 96.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.8
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.9 / Num. unique all: 9156 / % possible all: 88.7

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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 2A6Y

2a6y


Resolution: 1→10 Å / Num. parameters: 18836 / Num. restraintsaints: 22535 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.163 4953 5.3 %RANDOM
Rwork0.13 ---
obs0.13 94223 91.6 %-
all-94223 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2068.5
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 0 320 2093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0314
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.045
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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