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- PDB-6xsj: X-ray structure of a monoclinic form of alpha amylase from Asperg... -

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Basic information

Entry
Database: PDB / ID: 6xsj
TitleX-ray structure of a monoclinic form of alpha amylase from Aspergillus at 1.4 A resolution
ComponentsAlpha-amylase
KeywordsSUGAR BINDING PROTEIN / substrate complex / homology / catalytic site / Novo enzyme
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / carbohydrate catabolic process / alpha-amylase activity / 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
ALANINE / PHOSPHATE ION / Alpha-amylase / Alpha-amylase A type-1/2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 15, 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.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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,21513
Polymers109,6252
Non-polymers1,59011
Water22,6631258
1
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3875
Polymers54,8131
Non-polymers5754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8288
Polymers54,8131
Non-polymers1,0157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.983, 95.189, 74.988
Angle α, β, γ (deg.)90.000, 103.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-amylase /


Mass: 54812.746 Da / Num. of mol.: 2
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, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 7 types, 1267 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallized by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.10 M MES buffer. 8 ul Drops composed of equal amounts of enzyme in water at 30 mg/ml and the reservoir solution
PH range: 6.0 - 7.0

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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 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→76.7 Å / Num. obs: 307462 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Rrim(I) all: 0.163 / Rsym value: 0.152 / Net I/σ(I): 9.1
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 15076 / CC1/2: 0.98 / % possible all: 98.8

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Processing

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

2taa


Resolution: 1.4→72.91 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 7368 5.01 %
Rwork0.2022 139815 -
obs0.2039 147183 84.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.01 Å2 / Biso mean: 19.9776 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.4→72.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 218 1259 8843
Biso mean--53.44 29.18 -
Num. residues----952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.4262370.41989593216
1.42-1.430.3955600.3941943100318
1.43-1.450.441450.41891092113719
1.45-1.470.35191130.39031766187933
1.47-1.490.41971530.36782669282249
1.49-1.510.4161890.35153384357362
1.51-1.530.33882170.34013971418872
1.53-1.550.35882560.3244484474082
1.55-1.580.34172570.31354915517290
1.58-1.60.33762690.29835426569599
1.6-1.630.30352810.266855345815100
1.63-1.660.30552970.25754875784100
1.66-1.690.32312790.243354795758100
1.69-1.730.3012760.235955135789100
1.73-1.760.27522870.233555015788100
1.76-1.80.27112990.222555245823100
1.8-1.850.25342810.214154865767100
1.85-1.90.26122960.221254915787100
1.9-1.960.23432970.213655115808100
1.96-2.020.24523170.201454745791100
2.02-2.090.22972910.193555035794100
2.09-2.180.2262770.184755175794100
2.18-2.270.22392850.179455015786100
2.27-2.390.21813210.18454855806100
2.39-2.540.23392650.184155165781100
2.54-2.740.20792970.184455215818100
2.74-3.020.22012660.18655195785100
3.02-3.450.20612730.178755405813100
3.45-4.350.19592980.157555405838100
4.35-72.910.19542890.18856285917100

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