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- PDB-3ton: Crystral Structure of the C-terminal Subunit of Human Maltase-Glu... -

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Basic information

Entry
Database: PDB / ID: 3ton
TitleCrystral Structure of the C-terminal Subunit of Human Maltase-Glucoamylase
ComponentsMaltase-glucoamylase, intestinal
KeywordsHYDROLASE / Carbohydrate/Sugar Binding / Membrane
Function / homology
Function and homology information


amylase activity / dextrin catabolic process / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / maltose catabolic process / alpha-glucosidase / maltose alpha-glucosidase activity / starch catabolic process / Digestion of dietary carbohydrate / tertiary granule membrane ...amylase activity / dextrin catabolic process / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / maltose catabolic process / alpha-glucosidase / maltose alpha-glucosidase activity / starch catabolic process / Digestion of dietary carbohydrate / tertiary granule membrane / ficolin-1-rich granule membrane / catalytic activity / carbohydrate binding / apical plasma membrane / Neutrophil degranulation / extracellular exosome / plasma membrane
Similarity search - Function
: / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain ...: / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Few Secondary Structures / Irregular / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Maltase-glucoamylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.953 Å
AuthorsShen, Y. / Qin, X.H. / Ren, L.M.
CitationJournal: Protein Cell / Year: 2011
Title: Structural insight into substrate specificity of human intestinal maltase-glucoamylase
Authors: Ren, L.M. / Qin, X.H. / Cao, X.F. / Wang, L.L. / Bai, F. / Bai, G. / Shen, Y.
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltase-glucoamylase, intestinal
B: Maltase-glucoamylase, intestinal


Theoretical massNumber of molelcules
Total (without water)207,4542
Polymers207,4542
Non-polymers00
Water36020
1
A: Maltase-glucoamylase, intestinal


Theoretical massNumber of molelcules
Total (without water)103,7271
Polymers103,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltase-glucoamylase, intestinal


Theoretical massNumber of molelcules
Total (without water)103,7271
Polymers103,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.232, 106.232, 517.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 960:1849 )A0
211chain B and (resseq 960:1849 )B0

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Components

#1: Protein Maltase-glucoamylase, intestinal / / MGAM / Maltase / Alpha-glucosidase / Glucoamylase / Glucan 1 / 4-alpha-glucosidase


Mass: 103727.188 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 960-1853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAM / Production host: Pichia pastoris (fungus)
References: UniProt: O43451, alpha-glucosidase, glucan 1,4-alpha-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3M MgSO4, 16% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 50131 / Num. obs: 50131 / % possible obs: 78.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 44.65 Å2
Reflection shellResolution: 2.95→3.06 Å / % possible all: 78.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QLY

2qly


Resolution: 2.953→37.169 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7864 / SU ML: 0.36 / σ(F): 0 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 2353 5.02 %RANDOM
Rwork0.2321 ---
all0.2348 50131 --
obs0.2348 46866 73.54 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.229 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 153.33 Å2 / Biso mean: 58.6857 Å2 / Biso min: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.5014 Å20 Å2-0 Å2
2--14.5014 Å20 Å2
3----29.0028 Å2
Refinement stepCycle: LAST / Resolution: 2.953→37.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14250 0 0 20 14270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114698
X-RAY DIFFRACTIONf_angle_d1.30720052
X-RAY DIFFRACTIONf_chiral_restr0.0862114
X-RAY DIFFRACTIONf_plane_restr0.0062612
X-RAY DIFFRACTIONf_dihedral_angle_d16.7365254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7126X-RAY DIFFRACTIONPOSITIONAL0.043
12B7126X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9528-3.05830.4287660.36411230129621
3.0583-3.18070.4296760.30731704178029
3.1807-3.32540.34941440.29862581272543
3.3254-3.50060.3492260.2843955418167
3.5006-3.71970.3132860.25785190547687
3.7197-4.00660.27972780.22945656593494
4.0066-4.40920.27593110.18885816612796
4.4092-5.04590.21612770.17545936621397
5.0459-6.35220.26213270.21296025635298
6.3522-37.17220.29513620.26286420678299

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