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- PDB-7p4w: Crystal structure of alpha-amylase from Aspergillus oryzae in spa... -

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Basic information

Entry
Database: PDB / ID: 7p4w
TitleCrystal structure of alpha-amylase from Aspergillus oryzae in space group I222
ComponentsAlpha-amylase
KeywordsHYDROLASE / amylase / aspergillus / oryzae / alpha-amylase
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / calcium ion binding
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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBellini, D. / Gorrec, F.
CitationJournal: J.Appl.Crystallogr. / Year: 2022
Title: The FUSION protein crystallization screen.
Authors: Gorrec, F. / Bellini, D.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0124
Polymers52,3521
Non-polymers6603
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-2 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.725, 140.402, 154.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Alpha-amylase


Mass: 52351.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: A0A1S9DH83, alpha-amylase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 20k, 20% PEG 500mme, 0.1 M MES/Imidazole pH 6.5, 20 mM of each Polyamine (Morpheus Fusion screen, well H11)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→51.92 Å / Num. obs: 32915 / % possible obs: 99.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 9.9 / Rpim(I) all: 0.17 / Rrim(I) all: 4.9 / Net I/σ(I): 9.2
Reflection shellResolution: 2.28→2.32 Å / Rmerge(I) obs: 2.27 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1549 / CC1/2: 0.27 / Rpim(I) all: 1.1 / Rrim(I) all: 2.53

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TAA

6taa


Resolution: 2.28→51.91 Å / SU ML: 0.4488 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2851 1598 4.89 %
Rwork0.2283 31099 -
obs0.231 32697 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.44 Å2
Refinement stepCycle: LAST / Resolution: 2.28→51.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 58 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813821
X-RAY DIFFRACTIONf_angle_d1.13765218
X-RAY DIFFRACTIONf_chiral_restr0.0634574
X-RAY DIFFRACTIONf_plane_restr0.0085672
X-RAY DIFFRACTIONf_dihedral_angle_d8.5381540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.48441260.41632552X-RAY DIFFRACTION91.06
2.35-2.440.40911550.35232809X-RAY DIFFRACTION99.6
2.44-2.530.34581350.30612802X-RAY DIFFRACTION99.83
2.54-2.650.38191240.29072840X-RAY DIFFRACTION99.97
2.65-2.790.33521430.28672813X-RAY DIFFRACTION99.83
2.79-2.960.33311620.29962812X-RAY DIFFRACTION99.93
2.96-3.190.38421380.2842857X-RAY DIFFRACTION99.93
3.19-3.510.35021460.26222866X-RAY DIFFRACTION99.97
3.52-4.020.24111630.21592835X-RAY DIFFRACTION99.97
4.02-5.070.2381410.16072908X-RAY DIFFRACTION100
5.07-51.910.20521650.16423005X-RAY DIFFRACTION99.78

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