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- PDB-2xgi: Crystal structure of Barley Beta-Amylase complexed with 3,4- epox... -

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Basic information

Entry
Database: PDB / ID: 2xgi
TitleCrystal structure of Barley Beta-Amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside
ComponentsBETA-AMYLASE
KeywordsHYDROLASE / GLYCOSIDASE / CARBOHYDRATE METABOLISM / GLYCOSYL HYDROLASE FAMILY 14 / STARCH DEGRADATION / GERMINATION
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / : / polysaccharide catabolic process / identical protein binding
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
(3S)-3-hydroxybutyl alpha-D-glucopyranoside / (3R)-3-hydroxybutyl alpha-D-glucopyranoside / Beta-amylase
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRejzek, M. / Stevenson, C.E.M. / Southard, A.M. / Stanley, D. / Denyer, K. / Smith, A.M. / Naldrett, M.J. / Lawson, D.M. / Field, R.A.
CitationJournal: Mol Biosyst / Year: 2011
Title: Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley beta-amylase.
Authors: Rejzek, M. / Stevenson, C.E. / Southard, A.M. / Stanley, D. / Denyer, K. / Smith, A.M. / Naldrett, M.J. / Lawson, D.M. / Field, R.A.
History
DepositionJun 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Jan 11, 2012Group: Other
Revision 2.0Feb 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_biol / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.formula_weight / _entity.pdbx_description / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: 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
Remark 700 SHEET DETERMINATION METHOD: DSSP BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9- ... SHEET DETERMINATION METHOD: DSSP BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)60,2995
Polymers59,6701
Non-polymers6294
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.631, 71.158, 92.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-AMYLASE / 1 / 4-ALPHA-D-GLUCAN MALTOHYDROLASE


Mass: 59670.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PROTEIN PURCHASED FROM MEGAZYME / Source: (natural) HORDEUM VULGARE (barley) / Tissue: GRAIN ENDOSPERM / References: UniProt: P16098, beta-amylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-J5B / (3R)-3-hydroxybutyl alpha-D-glucopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-3-oxidanylbutoxy]oxane-3,4,5-triol / reacted 3,4-EPOXYBUTYL-ALPHA-D-GLUCOPYRANOSIDE / (3R)-3-hydroxybutyl alpha-D-glucoside / (3R)-3-hydroxybutyl D-glucoside / (3R)-3-hydroxybutyl glucoside


Type: D-saccharide / Mass: 252.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H20O7
#4: Sugar ChemComp-EBQ / (3S)-3-hydroxybutyl alpha-D-glucopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{S})-3-oxidanylbutoxy]oxane-3,4,5-triol / reacted 3R,4-EPOXYBUTYL-ALPHA-D-GLUCOPYRANOSIDE / (3S)-3-hydroxybutyl alpha-D-glucoside / (3S)-3-hydroxybutyl D-glucoside / (3S)-3-hydroxybutyl glucoside


Type: D-saccharide / Mass: 252.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H20O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3,4-EPOXYBUTYL ALPHA-D-GLUCOPYRANOSIDE: THE LIGAND WAS A MIXTURE OF TWO DIASTEREOISOMERS EPIMERIC ...3,4-EPOXYBUTYL ALPHA-D-GLUCOPYRANOSIDE: THE LIGAND WAS A MIXTURE OF TWO DIASTEREOISOMERS EPIMERIC AT THE 3 POSITION. I.E. 3R,S-3,4-EPOXYBUTYL ALPHA-D-GLUCOPYRANOSIDE. THIS WAS SOAKED INTO CRYSTALS AT 10 MM FOR 24 HOURS. BOTH OF THE DIASTEREOISOMERS REACT WITH THE PROTEIN GIVING COVALENT LINKS TO ATOM OE2 OF GLU 184. THE RESULTANT COMPLEX IS THEREFORE A MIXTURE OF TWO DIASTEREOISOMERS. 2S-2-HYDROXY-4-ALPHA-D-GLUCOPYRANOSYLOXY BUTOXY-GAMMA-CARBONYL-GLU184 (EBG-GLU184) HAS BEEN REFINED WITH AN OCCUPANCY OF 0.6 AND 2R-2-HYDROXY-4-ALPHA-D-GLUCOPYRANOSYLOXY BUTOXY-GAMMA-CARBONYL-GLU184 (EBQ-GLU184)HAS BEEN REFINED WITH AN OCCUPANCY OF 0.4. 1,2-ETHANEDIOL: PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT
Sequence detailsPROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS FROM UNIPROTKB DATABASE ENTRY P16098 AT ...PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS FROM UNIPROTKB DATABASE ENTRY P16098 AT THREE POSITIONS. THESE CHANGES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS AND ARE ATTRIBUTED TO NATURAL VARIATION

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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: 1.91 Å3/Da / Density % sol: 35.6 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 1.16→26.13 Å / Num. obs: 109532 / % possible obs: 98 % / Observed criterion σ(I): -9 / Redundancy: 6.48 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.21
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.48 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0091refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B1Y

1b1y


Resolution: 1.3→24.701 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.316 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1578 5424 5.03 %RANDOM
Rwork0.1279 ---
obs0.129 109295 98.075 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11 Å2
Baniso -1Baniso -2Baniso -3
1-0.304 Å20 Å20 Å2
2---0.038 Å20 Å2
3----0.267 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 42 721 4651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9555857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96924.018219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.161529
X-RAY DIFFRACTIONr_chiral_restr0.10.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.461.5991
X-RAY DIFFRACTIONr_mcbond_other0.631.5415
X-RAY DIFFRACTIONr_mcangle_it2.12721610
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1413629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3054.5599
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.80837243
X-RAY DIFFRACTIONr_sphericity_free7.9943741
X-RAY DIFFRACTIONr_sphericity_bonded3.99637100
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 290 -
Rwork0.31 6308 -
obs--81.306 %

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