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- PDB-6f9l: Crystal structure of Barley Beta-Amylase complexed with 3-Deoxy-3... -

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Basic information

Entry
Database: PDB / ID: 6f9l
TitleCrystal structure of Barley Beta-Amylase complexed with 3-Deoxy-3-fluoro-maltose
ComponentsBeta-amylase
KeywordsHYDROLASE / Edible Grain / Endosperm / Enzyme Inhibitors / Models / Molecular / Molecular Conformation / Starch / Structure-Activity Relationship / beta-Amylase
Function / homology
Function and homology information


amylopectin maltohydrolase activity / beta-amylase / beta-amylase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycoside hydrolase, family 14, conserved site / Glycosyl hydrolase family 14 / Beta-amylase active site 1. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-Deoxy-3-fluoro-maltose / Beta-amylase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTantanarat, K. / Stevenson, C.E.M. / Rejzek, M. / Lawson, D.M. / Field, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)BB/J004561/1 United Kingdom
CitationJournal: To be published
Title: Crystal structure of Barley Beta-Amylase complexed with 3-Deoxy-3-fluoro-maltose
Authors: Tantanarat, K. / Stevenson, C.E.M. / Rejzek, M. / Lawson, D.M. / Field, R.A.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0963
Polymers59,7161
Non-polymers3802
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.080, 99.410, 64.760
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-602-

CL

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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 / Details: Naturally occurring variant / Source: (natural) Hordeum vulgare (barley) / Variant: Glu165 / References: UniProt: A8CFR3, beta-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-3-deoxy-3-fluoro-alpha-D-glucopyranose / 3-Deoxy-3-fluoro-maltose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 344.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3-Deoxy-3-fluoro-maltose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_3*F][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp3fluoro]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% Polyacrylate, 100mM 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: 1.77→64.76 Å / Num. obs: 46468 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.034 / Rrim(I) all: 0.074 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.77-1.824.61.04133310.5740.541.17898
7.92-64.7640.0276130.9990.0150.03199.2

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XFR
Resolution: 1.77→64.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.324 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2293 5 %RANDOM
Rwork0.1591 ---
obs0.1611 43152 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.63 Å2 / Biso mean: 34.129 Å2 / Biso min: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.1 Å2
Refinement stepCycle: final / Resolution: 1.77→64.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 24 349 4250
Biso mean--43.42 41.6 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194064
X-RAY DIFFRACTIONr_bond_other_d0.0020.023629
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9485533
X-RAY DIFFRACTIONr_angle_other_deg0.99238433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54523.816207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69715645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 161 -
Rwork0.299 2694 -
all-2855 -
obs--83.97 %
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)
10.87021.15770.38461.54250.50780.17630.3975-0.47410.25140.4471-0.59080.31520.1773-0.19220.19330.229-0.12340.22030.3058-0.050.231812.276817.943828.216
20.19120.08470.27140.2705-0.3021.5583-0.055-0.07430.06050.00960.00770.0430.0003-0.14610.04730.08980.02770.02490.0592-0.01240.162712.81528.63616.1328
30.7729-0.14490.54470.16240.05960.5786-0.06510.00630.02270.01780.00440.0387-0.04780.00830.06070.08540.00050.00740.04160.00750.155518.910127.82186.6285
40.6008-0.2280.21590.9562-0.66170.50090.10920.1548-0.0976-0.06910.01820.23280.01350.0274-0.12740.0754-0.0075-0.04080.0724-0.0340.215313.785612.0995-11.6277
50.80850.30130.92630.43360.89071.9917-0.03580.0364-0.1054-0.01140.04930.0166-0.04840.111-0.01340.0797-0.00910.00260.0622-0.01630.162827.231819.60522.907
60.2680.04620.01060.29840.18670.5306-0.0069-0.0037-0.20170.0652-0.02240.06790.00760.02350.02930.0549-0.00320.03670.01680.01740.241718.27434.259913.6441
75.76354.846-5.10565.9285-4.07414.55130.295-0.0263-0.22980.5254-0.4448-0.519-0.2503-0.03370.14990.1619-0.023-0.00250.12590.10860.10727.562711.34431.7985
81.08430.3231-0.25450.49460.2871.0789-0.09060.0054-0.2314-0.01880.0765-0.0810.07990.17850.01410.02090.0120.01050.03650.01250.196529.52255.00778.5788
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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