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- PDB-4xqm: Crystal structure of the MRH domain of Glucosidase II beta bound ... -

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Basic information

Entry
Database: PDB / ID: 4xqm
TitleCrystal structure of the MRH domain of Glucosidase II beta bound to mannose
ComponentsGlucosidase 2 subunit beta
KeywordsHYDROLASE / sugar binding protein
Function / homology
Function and homology information


mannan binding / glucosidase II complex / N-glycan processing / enzyme-substrate adaptor activity / protein N-linked glycosylation / D-mannose binding / enzyme regulator activity / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily ...Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Low-density lipoprotein (LDL) receptor class A repeat / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Glucosidase 2 subunit beta
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.625 Å
AuthorsOlson, L.J. / Dahms, N.M. / Kim, J.-J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042667 United States
Mizutani Foundation for Glycoscience10-0056 United States
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structure and Functional Analyses of the Lectin Domain of Glucosidase II: Insights into Oligomannose Recognition.
Authors: Olson, L.J. / Orsi, R. / Peterson, F.C. / Parodi, A.J. / Kim, J.J. / D'Alessio, C. / Dahms, N.M.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Other
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_detector / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7242
Polymers10,5441
Non-polymers1801
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.571, 57.571, 58.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-673-

HOH

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Components

#1: Protein Glucosidase 2 subunit beta / Alpha-glucosidase 2 subunit beta


Mass: 10543.977 Da / Num. of mol.: 1 / Fragment: MRH domain (UNP residues 380-473)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: gtb1, gls2-beta, SPCC825.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USH8, EC: 3.2.1.84
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 10mg/ml protein in 20mM Tris pH 7.5, 150mM NaCl, 100mM mannose mixed 1:1 with 100 mM triethanolamine HCl pH 8.25, 200 mM potassium glutamate, 28% PEG 4000

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 12000 / % possible obs: 99 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.521 / Net I/av σ(I): 49.61 / Net I/σ(I): 14.5 / Num. measured all: 153936
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.62-1.653.70.3954671.19179.6
1.65-1.686.10.4166041.28299.5
1.68-1.719.10.4045951.296100
1.71-1.7511.20.3526111.491100
1.75-1.7812.60.3176201.489100
1.78-1.8213.30.2785841.393100
1.82-1.8713.50.2346121.688100
1.87-1.9213.80.1956111.832100
1.92-1.9813.90.1645841.653100
1.98-2.04140.1486041.619100
2.04-2.11140.1196061.651100
2.11-2.214.10.0946131.584100
2.2-2.314.10.0936011.523100
2.3-2.4214.30.086071.495100
2.42-2.5714.30.0676091.428100
2.57-2.7714.40.066101.359100
2.77-3.0514.50.0516011.517100
3.05-3.4914.50.0386121.478100
3.49-4.414.60.036141.38100
4.4-5014.30.036351.57499.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SHELXphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.625→29.161 Å / FOM work R set: 0.8862 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 2354 10.07 %
Rwork0.1673 21024 -
obs0.1703 23378 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.48 Å2 / Biso mean: 17.69 Å2 / Biso min: 9.11 Å2
Refinement stepCycle: final / Resolution: 1.625→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 12 142 891
Biso mean--18.56 27.24 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009764
X-RAY DIFFRACTIONf_angle_d1.3961027
X-RAY DIFFRACTIONf_chiral_restr0.09114
X-RAY DIFFRACTIONf_plane_restr0.004130
X-RAY DIFFRACTIONf_dihedral_angle_d12.802288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6251-1.65820.36611050.31561073117885
1.6582-1.69430.24321370.26991215135299
1.6943-1.73370.25841500.213212561406100
1.7337-1.7770.20111200.192612491369100
1.777-1.82510.2141400.184312631403100
1.8251-1.87880.18591400.175912341374100
1.8788-1.93940.22221440.175512701414100
1.9394-2.00870.19271420.171312321374100
2.0087-2.08910.23211420.18412581400100
2.0891-2.18410.19511520.153612291381100
2.1841-2.29930.21721380.164312461384100
2.2993-2.44320.20191350.165912411376100
2.4432-2.63180.23181420.16712841426100
2.6318-2.89640.21651320.163812361368100
2.8964-3.3150.18481420.162812531395100
3.315-4.17460.17051560.131612431399100
4.1746-29.16520.1421370.158112421379100

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