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- PDB-1gvi: Thermus maltogenic amylase in complex with beta-CD -

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Basic information

Entry
Database: PDB / ID: 1gvi
TitleThermus maltogenic amylase in complex with beta-CD
ComponentsMALTOGENIC AMYLASE
KeywordsHYDROLASE / AMYLASE / TRANSGLYCOSYLATION / BETA-CYCLODEXTRIN
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-cyclodextrin / Maltogenic amylase
Similarity search - Component
Biological speciesTHERMUS SP. (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 3.3 Å
AuthorsKim, M.-S. / Kim, J.-I. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Cyclomaltodextrinase, Neopullulanase, and Maltogenic Amylase are Nearly Indistinguishable from Each Other
Authors: Lee, H.-S. / Kim, M.-S. / Cho, H.-S. / Kim, J.-I. / Kim, T.-J. / Lee, H.-S. / Oh, B.-H. / Park, K.-H.
History
DepositionFeb 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOGENIC AMYLASE
B: MALTOGENIC AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8714
Polymers136,5652
Non-polymers2,3062
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-1.1 kcal/mol
Surface area54030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)119.090, 119.090, 270.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein MALTOGENIC AMYLASE


Mass: 68282.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O69007
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.8 / Method: vapor diffusion / Details: Kim, J.S., (1999) J. Biol. Chem., 274, 26279.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
216 mMmaleate1droppH6.8
30.1 Mlithium sulfate1drop
40.06 Mammonium sulfate1drop
50.02 Msodium citrate1drop
60.8 %(v/v)ethanol1drop
70.5 Mlithium sulfate1reservoir
80.3 Mammonium sulfate1reservoir
90.1 Msodium citrate1reservoirpH5.6
104 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 28949 / % possible obs: 89.4 % / Observed criterion σ(I): 1 / Redundancy: 2.5 %
Reflection
*PLUS
Num. obs: 32689 / % possible obs: 89.3 % / Num. measured all: 271781 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 81.4 % / Rmerge(I) obs: 0.26

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -5 %RANDOM
Rwork0.192 ---
obs0.192 28949 89.3 %-
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9656 0 154 0 9810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.481
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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