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- PDB-6f9j: Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha... -

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Basic information

Entry
Database: PDB / ID: 6f9j
TitleCrystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D-mannopyranosyl-(1-deoxynojirimycin)
ComponentsBeta-amylase
KeywordsHYDROLASE / Edible Grain / Endosperm / Enzyme Inhibitors / Models / Molecular / Molecular Conformation / Starch / Structure-Activity Relationship / beta-Amylase
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 / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / 1-DEOXYNOJIRIMYCIN / Beta-amylase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMoncayo, M.A. / Rodrigues, L.L. / Stevenson, C.E.M. / Ruzanski, C. / Rejzek, M. / Lawson, D.M. / Angulo, J. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)BB/J004561/1 United Kingdom
John Innes Foundation United Kingdom
Royal Society Newton Fund Fellowship United Kingdom
CitationJournal: To be published
Title: Synthesis, biological and structural analysis of prospective glycosyl-iminosugar prodrugs: impact on germination
Authors: Moncayo, M.A. / Rodrigues, L.L. / Stevenson, C.E.M. / Ruzanski, C. / Rejzek, M. / Lawson, D.M. / Angulo, J. / Field, R.A.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0954
Polymers59,7161
Non-polymers3793
Water5,567309
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint2 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.200, 99.320, 64.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-603-

CL

21A-960-

HOH

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Components

#1: Protein Beta-amylase /


Mass: 59716.195 Da / Num. of mol.: 1 / Mutation: D165E, L347S / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / References: UniProt: A8CFR3, beta-amylase
#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE / 1-Deoxynojirimycin


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
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
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% Polyacrylate, 100 mM Tris pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2013
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.67→73.2 Å / Num. obs: 54088 / % possible obs: 98 % / Redundancy: 8 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.021 / Rrim(I) all: 0.063 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.67-1.717.51.04140160.6310.4021.12399.2
7.47-73.27.20.0286750.9980.0110.0394.6

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XFR
Resolution: 1.67→73.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.004 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 2601 5.1 %RANDOM
Rwork0.1619 ---
obs0.1636 48428 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.82 Å2 / Biso mean: 33.477 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---1.69 Å20 Å2
3---2.73 Å2
Refinement stepCycle: final / Resolution: 1.67→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 23 310 4200
Biso mean--31.81 39.62 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194085
X-RAY DIFFRACTIONr_bond_other_d0.0020.023640
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9465559
X-RAY DIFFRACTIONr_angle_other_deg0.97938453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54623.854205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181527
X-RAY DIFFRACTIONr_chiral_restr0.0840.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02884
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 166 -
Rwork0.271 3035 -
all-3201 -
obs--79.02 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.55660.3441-0.37431.80510.66180.76380.129-0.1513-0.04180.2608-0.32090.18110.0644-0.03220.19190.1578-0.05570.11780.0783-0.01370.140112.345617.907728.2711
20.14950.14740.19280.275-0.14521.1921-0.026-0.05250.04880.0112-0.03180.0524-0.0349-0.10850.05780.14020.01860.02720.0376-0.00820.166212.829828.58816.2167
30.5537-0.07520.57720.22150.06060.694-0.05940.01980.03550.0249-0.01130.0384-0.0440.01840.07070.1267-0.00190.00720.03390.00710.157118.918927.79626.6559
40.4872-0.4086-0.01891.0936-0.46780.33790.06530.0803-0.0714-0.11090.01090.1455-0.005-0.0251-0.07620.0938-0.026-0.01310.0579-0.04620.187713.933212.3593-11.5936
50.68440.32740.74020.28920.64511.4468-0.04250.0059-0.1247-0.0240.0351-0.0045-0.07430.07250.00750.1221-0.00880.00990.0436-0.00760.170327.228219.58822.8676
60.15890.11580.020.31460.22950.52370.0126-0.001-0.15340.0754-0.02840.01650.0276-0.00110.01580.1077-0.010.03470.0127-0.0070.261618.33754.273913.5822
77.04976.3549-6.39097.5064-6.74066.33620.3015-0.05490.03870.3552-0.25440.0252-0.31590.1496-0.04710.1689-0.0180.01020.08010.07490.099527.659411.289431.776
80.81620.3071-0.31240.48040.41210.8889-0.0718-0.0042-0.21750.01140.0785-0.14790.07940.1207-0.00670.08240.0190.00140.02590.01420.206529.56625.01858.5012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 47
2X-RAY DIFFRACTION2A48 - 114
3X-RAY DIFFRACTION3A115 - 186
4X-RAY DIFFRACTION4A187 - 256
5X-RAY DIFFRACTION5A257 - 289
6X-RAY DIFFRACTION6A290 - 442
7X-RAY DIFFRACTION7A443 - 453
8X-RAY DIFFRACTION8A454 - 489

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