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- PDB-7taa: FAMILY 13 ALPHA AMYLASE IN COMPLEX WITH ACARBOSE -

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Basic information

Entry
Database: PDB / ID: 7taa
TitleFAMILY 13 ALPHA AMYLASE IN COMPLEX WITH ACARBOSE
ComponentsTAKA AMYLASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / TAKA / AMYLASE / ACARBOSE
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MODIFIED ACARBOSE HEXASACCHARIDE / Alpha-amylase A type-1/2 / Alpha-amylase A type-3
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / NATIVE STRUCTURE / Resolution: 1.98 Å
AuthorsDavies, G.J. / Brzozowski, A.M.
CitationJournal: Biochemistry / Year: 1997
Title: Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
Authors: Brzozowski, A.M. / Davies, G.J.
History
DepositionOct 6, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAKA AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5043
Polymers52,5261
Non-polymers9782
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.040, 67.183, 133.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TAKA AMYLASE


Mass: 52525.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold)
References: UniProt: P10529, UniProt: P0C1B3*PLUS, alpha-amylase
#2: Sugar ChemComp-ABC / MODIFIED ACARBOSE HEXASACCHARIDE


Type: saccharide / Mass: 937.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C37H63NO26
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 18% MM PEG 5000, 5MM CALCIUM CHLORIDE, 0.1M HEPES BUFFER, PH 7.5. METHOD: HANGING DROP VAPOUR DIFFUSION. THE NATIVE CRYSTALS WERE SOAKED FOR 6 HOURS IN STABILIZING SOLUTION CONTAINING 15 MM ...Details: 18% MM PEG 5000, 5MM CALCIUM CHLORIDE, 0.1M HEPES BUFFER, PH 7.5. METHOD: HANGING DROP VAPOUR DIFFUSION. THE NATIVE CRYSTALS WERE SOAKED FOR 6 HOURS IN STABILIZING SOLUTION CONTAINING 15 MM OF ACARBOSE., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MHEPES-HCl1reservoir
25 mM1reservoirCaCl2
316-18 %(w/v)mPEG5000 MW1reservoir
410 mMTris-HCl1drop
55 mM1dropCaCl2
630 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1995 / Details: LONG MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 63935 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.1 / % possible all: 94.2
Reflection
*PLUS
Num. obs: 31062 / Num. measured all: 113411
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
AGROVATA(CCP4)data reduction
REFMACrefinement
AGROVATAdata scaling
RefinementMethod to determine structure: NATIVE STRUCTURE / Resolution: 1.98→20 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1553 5 %RANDOM
Rwork0.159 ---
obs-31015 97 %-
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 66 465 4219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.2664
X-RAY DIFFRACTIONp_mcangle_it3.9416
X-RAY DIFFRACTIONp_scbond_it4.1836
X-RAY DIFFRACTIONp_scangle_it5.4238
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.1840.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1730.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor18.320
X-RAY DIFFRACTIONp_orthonormal_tor34.925
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 1.98→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 -5 %
Rwork0.194 3063 -
obs--94.2 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

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