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- PDB-3bsh: Barley alpha-amylase isozyme 1 (AMY1) double mutant Y105A/Y380A i... -

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Basic information

Entry
Database: PDB / ID: 3bsh
TitleBarley alpha-amylase isozyme 1 (AMY1) double mutant Y105A/Y380A in complex with inhibitor acarbose
ComponentsAlpha-amylase type A isozyme
KeywordsHYDROLASE / barley alpha-amylase / AMY1 / mutant / acarbose / complex / Calcium / Carbohydrate metabolism / Germination / Glycosidase / Metal-binding / Secreted
Function / homology
Function and homology information


starch catabolic process / alpha-amylase / alpha-amylase activity / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, C-terminal beta-sheet / Alpha-amylase, plant / Alpha-amylase C-terminal beta-sheet domain / Alpha-amylase C-terminal beta-sheet domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal beta-sheet / Alpha-amylase, plant / Alpha-amylase C-terminal beta-sheet domain / Alpha-amylase C-terminal beta-sheet domain / 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
beta-D-glucopyranose / Alpha-amylase type A isozyme
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsAghajari, N. / Robert, X. / Haser, R.
CitationJournal: Febs Lett. / Year: 2008
Title: Multi-site substrate binding and interplay in barley alpha-amylase 1
Authors: Nielsen, M.M. / Seo, E.S. / Bozonnet, S. / Aghajari, N. / Robert, X. / Haser, R. / Svensson, B.
History
DepositionDec 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase type A isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6135
Polymers45,3131
Non-polymers3004
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.500, 72.100, 60.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

21A-955-

HOH

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Components

#1: Protein Alpha-amylase type A isozyme / alpha-amylase isozyme 1 / 1 / 4-alpha-D- glucan glucanohydrolase / AMY1 / Low pI alpha-amylase


Mass: 45312.812 Da / Num. of mol.: 1 / Mutation: Y105A, Y380A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pPICZA / Production host: Pichia pastoris (fungus) / References: UniProt: P00693, alpha-amylase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS CONFIRM THAT THIS RESIDUE IS VAL AND DATABASE SEQUENCE IS INCORRECT AT THIS POSITION.

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES buffer pH 7.5, 20%(w/v) PEG 8000, 3% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: synchrotron mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 9152 / Num. obs: 9224 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rsym value: 0.143 / Net I/σ(I): 11.23
Reflection shellHighest resolution: 3 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 10.29 / Num. unique all: 7949 / Rsym value: 0.155 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HT6

1ht6


Resolution: 3→29.19 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2758484.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 491 5.4 %RANDOM
Rwork0.197 ---
obs0.197 9143 99.3 %-
all-9143 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.4316 Å2 / ksol: 0.26974 e/Å3
Displacement parametersBiso mean: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.46 Å20 Å20 Å2
2---3.83 Å20 Å2
3----5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 3→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 15 112 3253
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.242
X-RAY DIFFRACTIONc_scangle_it1.852.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 63 4.2 %
Rwork0.248 1433 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4DAF_GLC.paramDAF_GLC.top

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