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- PDB-6xsv: X-ray structure of a tetragonal crystal form of alpha amylase fro... -

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Basic information

Entry
Database: PDB / ID: 6xsv
TitleX-ray structure of a tetragonal crystal form of alpha amylase from Aspergillus oryzae (Tala-Amylase) at 1.65 A resolution
ComponentsAlpha-amylase
KeywordsSUGAR BINDING PROTEIN / substrate complex / Novo lipase / catalytic site / ligands
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / alpha-amylase activity / carbohydrate catabolic process / calcium ion binding / extracellular region
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
alpha-D-mannopyranose / PALMITIC ACID / Alpha-amylase / Alpha-amylase A type-1/2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMcPherson, A.
CitationJournal: J.Biosci.Bioeng. / Year: 2021
Title: Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase).
Authors: Gee, C.L. / Holton, J.M. / McPherson, A.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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)56,3649
Polymers54,8131
Non-polymers1,5518
Water9,242513
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.126, 63.126, 265.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase


Mass: 54812.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: rhaG, amy3, OAory_01056410 / Production host: Aspergillus oryzae (mold)
References: UniProt: B0FZ76, UniProt: P0C1B3*PLUS, alpha-amylase

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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 517 molecules

#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: 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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.1 % / Description: elongated rectangular prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops composed of equal amounts of the protein at 30 ...Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops composed of equal amounts of the protein at 30 mg/ml in water with the reservoir solution. Crystals grew after about 0ne to two weeks at 298 K
PH range: 6 - 7.247

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→66.45 Å / Num. obs: 66065 / % possible obs: 99.8 % / Redundancy: 124.3 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.027 / Rrim(I) all: 0.141 / Rsym value: 0.128 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 41 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3098 / CC1/2: 0.19 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
SIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TAA

2taa


Resolution: 1.65→66.45 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 23.22 / Stereochemistry target values: ML
Details: Structure was refined to convergence in REFMAC then passed through ten runs of COOT rebuilding and REFINE from PHENIX.
RfactorNum. reflection% reflection
Rfree0.2048 3309 5.02 %
Rwork0.1746 62646 -
obs0.1762 65955 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.31 Å2 / Biso mean: 43.223 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.65→66.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 217 517 4417
Biso mean--75.66 43.87 -
Num. residues----476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.36391220.3612467258997
1.67-1.70.35081340.34262572270699
1.7-1.720.30221140.32612534264899
1.72-1.750.31931470.300825852732100
1.75-1.780.33291310.275625462677100
1.78-1.820.28351460.262125592705100
1.82-1.850.25791230.24325852708100
1.85-1.890.25941270.234625772704100
1.89-1.930.27231250.230725932718100
1.93-1.970.24231450.229726012746100
1.97-2.020.25911280.217525602688100
2.02-2.080.23681400.205925922732100
2.08-2.140.23561430.201825772720100
2.14-2.210.24261400.193725892729100
2.21-2.290.20631420.186425972739100
2.29-2.380.21291280.179326032731100
2.38-2.490.23841300.177126392769100
2.49-2.620.19461370.171226402777100
2.62-2.780.21861640.181825922756100
2.78-30.22041460.174526432789100
3-3.30.21631470.166726612808100
3.3-3.780.18421500.15326692819100
3.78-4.760.16041460.126627292875100
4.76-66.450.16641540.160129363090100

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