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- PDB-1sma: CRYSTAL STRUCTURE OF A MALTOGENIC AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1sma
TitleCRYSTAL STRUCTURE OF A MALTOGENIC AMYLASE
ComponentsMALTOGENIC AMYLASE
KeywordsHYDROLASE / AMYLASE / TRANSGLYCOSYLATION / 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
Biological speciesThermus sp. IM6501 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsKim, J.S. / Cha, S.S. / Oh, B.H.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of a maltogenic amylase provides insights into a catalytic versatility.
Authors: Kim, J.S. / Cha, S.S. / Kim, H.J. / Kim, T.J. / Ha, N.C. / Oh, S.T. / Cho, H.S. / Cho, M.J. / Kim, M.J. / Lee, H.S. / Kim, J.W. / Choi, K.Y. / Park, K.H. / Oh, B.H.
History
DepositionApr 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTOGENIC AMYLASE
B: MALTOGENIC AMYLASE


Theoretical massNumber of molelcules
Total (without water)136,5962
Polymers136,5962
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-4 kcal/mol
Surface area42730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.370, 118.370, 266.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.49959, -0.86626, -4.0E-5), (-0.86626, -0.49959, 0.00035), (-0.00032, -0.00014, -1)
Vector: 59.0504, 102.21605, 39.08575)

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Components

#1: Protein MALTOGENIC AMYLASE


Mass: 68298.242 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, BARREL, C-DOMAIN / Source method: isolated from a natural source / Source: (natural) Thermus sp. IM6501 (bacteria) / Strain: M6501 / References: UniProt: O69007
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.95 Å3/Da / Density % sol: 63 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
216 mMmaleate1drop
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 citrate1reservoir
104 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 40688 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Rsym value: 0.037
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4 %
Reflection shell
*PLUS
% possible obs: 87.3 % / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 --RANDOM
Rwork0.209 ---
obs0.209 40866 94.8 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11488 0 0 573 12061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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