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- PDB-6ger: Wheat b-amylase, a clinically relevant food allergen -

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Basic information

Entry
Database: PDB / ID: 6ger
TitleWheat b-amylase, a clinically relevant food allergen
ComponentsBeta-amylase
KeywordsHYDROLASE / TIM barrel / wheat allergen / food allergen
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-amylase Tri a 17
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.00004665055 Å
AuthorsHofer, G. / Keller, W.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundF4604 Austria
Austrian Science FundF4605 Austria
Citation
Journal: Allergy / Year: 2019
Title: Three-dimensional structure of the wheat beta-amylase Tri a 17, a clinically relevant food allergen.
Authors: Hofer, G. / Wieser, S. / Bogdos, M.K. / Gattinger, P. / Nakamura, R. / Ebisawa, M. / Makela, M. / Papadopoulos, N. / Valenta, R. / Keller, W.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _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: Beta-amylase


Theoretical massNumber of molelcules
Total (without water)57,5061
Polymers57,5061
Non-polymers00
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.870, 93.870, 65.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Beta-amylase / 1 / 4-alpha-D-glucan maltohydrolase


Mass: 57505.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag, 2 N-terminal amino acids and 19 C-terminal amino acids are not visible in the 2Fo-Fc map
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: BMY1, AMY1 / Production host: Escherichia coli (E. coli) / References: UniProt: P93594, beta-amylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG 3350 100mM bis-Tris pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2→27.0624427634 Å / Num. obs: 38550 / % possible obs: 92.28 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.3723010428 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.1203 / Rpim(I) all: 0.06928 / Rrim(I) all: 0.1394 / Net I/σ(I): 6.93
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2861 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 3721 / CC1/2: 0.906 / Rpim(I) all: 0.1676 / Rrim(I) all: 0.2861 / % possible all: 96.95

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 2.00004665055→27.0624427634 Å / SU ML: 0.143740860342 / Cross valid method: FREE R-VALUE / σ(F): 1.33355430453 / Phase error: 17.5477169956
RfactorNum. reflection% reflection
Rfree0.1886 1253 3.54 %
Rwork0.1582 --
obs-38550 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.96 Å2
Refinement stepCycle: LAST / Resolution: 2.00004665055→27.0624427634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 0 515 4400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002516603539974064
X-RAY DIFFRACTIONf_angle_d0.5419468497735523
X-RAY DIFFRACTIONf_chiral_restr0.0393566398504572
X-RAY DIFFRACTIONf_plane_restr0.00338276142065731
X-RAY DIFFRACTIONf_dihedral_angle_d15.87796390632433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.2065134298421300.1803430083793593X-RAY DIFFRACTION99.8123324397
2.0801-2.17470.1994831006141410.1741922130963829X-RAY DIFFRACTION99.8993457474
2.1747-2.28930.4411817088571000.3643324512362834X-RAY DIFFRACTION68.1374825824
2.2893-2.43270.2319091995291510.1733650937514102X-RAY DIFFRACTION99.3923813975
2.4327-2.62040.1755131456631480.1540672430544134X-RAY DIFFRACTION99.7670083877
2.6204-2.88380.2050839279641400.1493243060043775X-RAY DIFFRACTION90.8774373259
2.8838-3.30040.1775418538291580.1404476739154160X-RAY DIFFRACTION99.9768464922
3.3004-4.15580.1697959822961300.1331633403783584X-RAY DIFFRACTION85.7736720554
4.1558-27.06490.1453840522271590.1216158803034258X-RAY DIFFRACTION99.9773653237
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4946571656470.194979816954-0.04708978404580.69499295631-0.3431339563410.614934073038-0.0204474287092-0.0869039184606-0.0109464976250.3739990247730.07207018078590.1556304280570.1255791486480.0630932421448-0.02522858032740.2018604189930.03011570658450.03117907805870.07596054069140.01153562283280.0929818640466136.5253962-80.049232374614.332645064
20.8443129439220.172366743018-0.1062287866430.7666275594410.2024046689210.9862509144160.00197829830192-0.0144325249740.02452418068730.0601402575432-0.007458560890760.00791389313802-0.01015178862850.03628153020560.009527732762010.09703005520370.01450085993520.007583961697760.0468073200372-0.001269641704440.0513929584056140.640133898-66.81048480512.62853954366
32.844845996740.338324529161-1.368893871571.37009208776-0.2336925090972.67906470348-0.05248991632850.07339094548810.10842926509-0.1268897609740.03662047092440.146555979527-0.0600296392511-0.0425010506866-0.01844701899370.08885358655780.0384559396557-0.02435638125980.0794446396310.0186553697150.0909671064859128.902649425-61.6719432444-15.3812766048
42.285150419040.130036509905-0.7880659791810.878539663015-0.1384499959741.737169572690.00873508256730.4384177398130.15463044532-0.2099970568040.1171759594370.380941095203-0.132227139671-0.313157745158-0.05053825810690.1866866159230.0354757690686-0.09138127827740.217619937610.03915140922510.236321594999119.676593815-64.5861616057-22.0043638438
51.38179035136-0.1652875531580.1962390539830.738912053525-0.06368036265980.682183348387-0.009422056781580.09831708210910.00302789114771-0.08375212780640.01060684486680.088162267058-0.0251730977299-0.0352800109537-0.006427217674690.1007213187910.0128318149188-0.008909219536990.0603027071992-0.01535120642370.0562860720124134.606091909-74.5173115307-11.7320867693
60.4437641334130.100929568503-0.1867702236320.673993855594-0.06700967566990.556941679619-0.01869136770280.00258730344667-0.12034407913-0.0447649135186.41819510919E-50.1422470340450.109889604098-0.1117967434440.01876452822270.146949294778-0.0140512228786-0.01353510910490.104178754431-0.01469433346370.110756260606130.370477114-80.5550147008-11.2778469715
70.5394356795530.164461722439-0.09369437975060.767305747234-0.1081976272531.16049881028-0.04785595485790.00163687403778-0.03667054145780.06414923263490.03675233840980.2970474601630.197156989566-0.270858901505-0.0168451166060.147750991212-0.02209161826270.01635348907250.1275428587720.006510064525090.176871157612124.135485453-89.1157935554-2.68038080118
80.9920973344620.134278422264-0.1690852390221.255607015040.1798738049891.59286305509-0.00418093456937-0.171233632625-0.05923715715720.105934336757-0.02441594175630.3347142878910.0900151973328-0.2016989878280.005276021337570.210744137860.007111990553050.05410002145370.1029391523780.02982638034640.149758766883127.793523597-89.475207971710.821970372
90.6019978261570.146291162481-0.02943798375890.942016625348-0.6756030610051.34217236798-0.02670134805220.0314238643234-0.065117297747-0.100550657120.02790743064540.130187774720.189790438551-0.1652991435570.003106099785990.2127951395690.01834956857560.01100960795440.0472191079491-0.03925909456310.168059416987135.179741621-90.382728224-6.44780007674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 221 )
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 254 )
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 306 )
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 345 )
7X-RAY DIFFRACTION7chain 'A' and (resid 346 through 406 )
8X-RAY DIFFRACTION8chain 'A' and (resid 407 through 439 )
9X-RAY DIFFRACTION9chain 'A' and (resid 440 through 490 )

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