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

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Basic information

Entry
Database: PDB / ID: 3top
TitleCrystral Structure of the C-terminal Subunit of Human Maltase-Glucoamylase in Complex with Acarbose
ComponentsMaltase-glucoamylase, intestinal
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Membrane / HYDROLASE-HYDROLASE INHIBITOR complex
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
alpha-acarbose / Maltase-glucoamylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.881 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)208,7464
Polymers207,4542
Non-polymers1,2912
Water68538
1
A: Maltase-glucoamylase, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3732
Polymers103,7271
Non-polymers6461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltase-glucoamylase, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3732
Polymers103,7271
Non-polymers6461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.501, 105.501, 516.561
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: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 M 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: 2.88→50 Å / Num. all: 59475 / Num. obs: 59475 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 56.43 Å2
Reflection shellResolution: 2.88→2.98 Å / % possible all: 87.9

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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: 2.881→36.447 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7353 / SU ML: 0.39 / σ(F): 0 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 2830 5.09 %RANDOM
Rwork0.2185 ---
all0.2219 59475 --
obs0.2219 55586 82.33 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.276 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 225.53 Å2 / Biso mean: 87.5677 Å2 / Biso min: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-18.2351 Å20 Å2-0 Å2
2--18.2351 Å20 Å2
3----36.4701 Å2
Refinement stepCycle: LAST / Resolution: 2.881→36.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14262 0 88 38 14388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914804
X-RAY DIFFRACTIONf_angle_d1.26820206
X-RAY DIFFRACTIONf_chiral_restr0.0842152
X-RAY DIFFRACTIONf_plane_restr0.0062614
X-RAY DIFFRACTIONf_dihedral_angle_d17.4025436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7132X-RAY DIFFRACTIONPOSITIONAL0.04
12B7132X-RAY DIFFRACTIONPOSITIONAL0.04
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 (%)
2.8806-2.98350.52981130.40652286239936
2.9835-3.10290.49191710.29663031320248
3.1029-3.24410.38492150.29544097431265
3.2441-3.4150.36392900.2735377566785
3.415-3.62880.31583040.25265937624193
3.6288-3.90870.27653470.21866087643496
3.9087-4.30140.25293440.17716226657098
4.3014-4.92260.22693430.14796348669199
4.9226-6.1970.21643530.176865236876100
6.197-36.45040.30393500.252768447194100
Refinement TLS params.Method: refined / Origin x: -41.3889 Å / Origin y: 12.2699 Å / Origin z: -16.2605 Å
111213212223313233
T0.1722 Å20.0624 Å2-0.0221 Å2-0.3616 Å20.0341 Å2--0.3576 Å2
L0.0956 °20.0633 °20.3946 °2-0.2328 °20.1347 °2--1.3939 °2
S-0.0056 Å °0.0207 Å °-0.0442 Å °-0.198 Å °0.0195 Å °-0.0483 Å °0.1341 Å °0.4458 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA960 - 1849
2X-RAY DIFFRACTION1allB960 - 1849
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allA1
5X-RAY DIFFRACTION1allA1 - 40

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