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- PDB-1ht6: CRYSTAL STRUCTURE AT 1.5A RESOLUTION OF THE BARLEY ALPHA-AMYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1ht6
TitleCRYSTAL STRUCTURE AT 1.5A RESOLUTION OF THE BARLEY ALPHA-AMYLASE ISOZYME 1
ComponentsALPHA-AMYLASE ISOZYME 1
KeywordsHYDROLASE / BARLEY / ALPHA-AMYLASE / ISOZYME 1 / BETA-ALPHA-BARREL
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
Alpha-amylase type A isozyme
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRobert, X. / Haser, R. / Aghajari, N.
Citation
Journal: Structure / Year: 2003
Title: The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs
Authors: Robert, X. / Haser, R. / Gottschalk, T.E. / Ratajczak, F. / Driguez, H. / Svensson, B. / Aghajari, N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal and molecular structure of barley alpha-amylase
Authors: Kadziola, A. / Abe, J. / Svensson, B. / Haser, R.
History
DepositionDec 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-AMYLASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,31913
Polymers44,6401
Non-polymers67912
Water14,574809
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.360, 72.820, 61.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALPHA-AMYLASE ISOZYME 1 / AMY1


Mass: 44640.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Pichia pastoris (fungus) / References: UniProt: P00693, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 8000, ISOPROPANOL, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: Robert, X., (2002) Acta Crystallogr., D58, 683.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.1 mg/mlprotein1drop
23 %(v/v)2-propanol1drop
320 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9761 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2000 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 1.5→41.6 Å / Num. all: 271695 / Num. obs: 63366 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6.2 / Redundancy: 4.3 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 6.2 / Num. unique all: 4566 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 271695
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 97.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMY1 structure solved at 2.0A resolution (unpublished results)

Resolution: 1.5→41.56 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1597709.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 6.2 / Stereochemistry target values: Engh & Huber
Details: THE C-TERMINAL RESIDUE ASN 405 WAS NOT SEEN IN DENSITY. RESIDUES 406 TO 414 WERE NOT LOCATED IN THE STRUCTURE BECAUSE OF THEIR INTENTIONAL TRUNCATION DURING THE MOLECULAR BIOLOGY ENGINEERING.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 6406 10.1 %RANDOM
Rwork0.136 ---
all-64482 --
obs-63346 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.01 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---1.31 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 39 809 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.173 1065 10.3 %
Rwork0.144 9296 -
obs-9296 97.7 %
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 DIFFRACTION4LIGAND.PARAMLIGAND.TOP
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 41.6 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.54 Å

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