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- PDB-3wn6: Crystal structure of alpha-amylase AmyI-1 from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 3wn6
TitleCrystal structure of alpha-amylase AmyI-1 from Oryza sativa
ComponentsAlpha-amylase
KeywordsHYDROLASE / (alpha/beta)8-barrel / Carbohydrate/Sugar Binding / Glycosylation
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / starch catabolic process / sucrose catabolic process / alpha-amylase / alpha-amylase activity / calcium ion binding
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
DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / Alpha-amylase
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsOchiai, A. / Sugai, H. / Harada, K. / Tanaka, S. / Ishiyama, Y. / Ito, K. / Tanaka, T. / Uchiumi, T. / Taniguchi, M. / Mitsui, T.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2014
Title: Crystal structure of alpha-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability
Authors: Ochiai, A. / Sugai, H. / Harada, K. / Tanaka, S. / Ishiyama, Y. / Ito, K. / Tanaka, T. / Uchiumi, T. / Taniguchi, M. / Mitsui, T.
History
DepositionDec 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-amylase
B: Alpha-amylase
C: Alpha-amylase
D: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,32338
Polymers181,3704
Non-polymers2,95334
Water29,3641630
1
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15910
Polymers45,3431
Non-polymers8179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9959
Polymers45,3431
Non-polymers6538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9478
Polymers45,3431
Non-polymers6057
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,22211
Polymers45,3431
Non-polymers87910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.917, 125.277, 96.642
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 25 - 428 / Label seq-ID: 1 - 404

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha-amylase / 1 / 4-alpha-D-glucan glucanohydrolase / Alpha-amylase isozyme 1B


Mass: 45342.574 Da / Num. of mol.: 4 / Mutation: G25M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: AMY1.1, AMY1A / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P17654, alpha-amylase

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Non-polymers , 5 types, 1664 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1630 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 2% tacsimate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.551
11h,-k,-l20.449
ReflectionResolution: 2.1→50 Å / Num. obs: 97842 / % possible obs: 98.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9 / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG9

1bg9


Resolution: 2.16→48.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.644 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24323 4418 5 %RANDOM
Rwork0.19937 ---
obs0.20161 83885 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.099 Å2
Baniso -1Baniso -2Baniso -3
1--15.91 Å20 Å2-2.2 Å2
2---22.2 Å2-0 Å2
3---38.11 Å2
Refinement stepCycle: LAST / Resolution: 2.16→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12812 0 175 1630 14617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913518
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212228
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.93118365
X-RAY DIFFRACTIONr_angle_other_deg1.044328165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15751651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93424.21677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.214152063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2431570
X-RAY DIFFRACTIONr_chiral_restr0.0890.21848
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115647
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023287
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A248510.07
12B248510.07
21A248460.06
22C248460.06
31A248360.07
32D248360.07
41B249340.07
42C249340.07
51B249310.06
52D249310.06
61C246540.07
62D246540.07
LS refinement shellResolution: 2.162→2.219 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 283 -
Rwork0.21 5194 -
obs-5194 82.08 %

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