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- PDB-1rp8: Crystal structure of barley alpha-amylase isozyme 1 (amy1) inacti... -

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Basic information

Entry
Database: PDB / ID: 1rp8
TitleCrystal structure of barley alpha-amylase isozyme 1 (amy1) inactive mutant d180a in complex with maltoheptaose
ComponentsAlpha-amylase type 1 isozyme
KeywordsHYDROLASE / ALPHA-AMYLASE / BARLEY / ISOZYME 1 / INACTIVE MUTANT / BETA-ALPHA-BARREL / SUGAR TONGS BINDING SITE / MALTOHEPTAOSE / MALTOPENTAOSE
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-maltopentaose / Alpha-amylase type A isozyme
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER DIFFERENCE / Resolution: 2 Å
AuthorsRobert, X. / Haser, R. / Aghajari, N.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Oligosaccharide Binding to Barley {alpha}-Amylase 1
Authors: Robert, X. / Haser, R. / Mori, H. / Svensson, B. / Aghajari, N.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 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 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE ACCORDING TO THE AUTHORS, THERE IS AN ERROR IN SWISSPROT DATABASE, CORRECTED BY ...SEQUENCE ACCORDING TO THE AUTHORS, THERE IS AN ERROR IN SWISSPROT DATABASE, CORRECTED BY EXAMINATION OF THE CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase type 1 isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5277
Polymers44,5961
Non-polymers2,9316
Water9,926551
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.000, 72.500, 62.180
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 type 1 isozyme / 1 / 4-alpha-D-glucan glucanohydrolase / AMY1 / Low pI alpha-amylase


Mass: 44596.047 Da / Num. of mol.: 1 / Mutation: D180A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: AMY1.1 / Plasmid: pPICZA / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P00693, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1a_1-5][a2122h-1b_1-5]/1-1-1-1-2-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 8000, ISOPROPANOL, pH 6.7, 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: MARRESEARCH / Detector: CCD / Date: Dec 13, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→39.14 Å / Num. all: 29146 / Num. obs: 29146 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 5.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2104 / Rsym value: 0.311 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER DIFFERENCE
Starting model: PDB ENTRY 1HT6

1ht6


Resolution: 2→39.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1832571.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2900 10 %RANDOM
Rwork0.172 ---
all0.172 29146 --
obs0.172 29095 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7586 Å2 / ksol: 0.3784 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 193 551 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 483 10.1 %
Rwork0.197 4282 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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