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

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Basic information

Entry
Database: PDB / ID: 2xgb
TitleCrystal structure of Barley Beta-Amylase complexed with 2,3- epoxypropyl-alpha-D-glucopyranoside
ComponentsBETA-AMYLASE
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / GERMINATION
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding
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
(2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside / Beta-amylase
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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 1.5Dec 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 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS 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

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Assembly

Deposited unit
A: BETA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1556
Polymers59,6701
Non-polymers4845
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.622, 71.068, 92.309
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: Sugar ChemComp-EPG / (2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside / 2-HYDROXYMETHYL-6-OXIRANYLMETHOXY-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 2,3-EPOXYPROPYL-ALPHA-D-GLUCOPYRANOSIDE / (2R)-oxiran-2-ylmethyl alpha-D-glucoside / (2R)-oxiran-2-ylmethyl D-glucoside / (2R)-oxiran-2-ylmethyl glucoside


Type: D-saccharide / Mass: 236.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H16O7
IdentifierTypeProgram
2,3-epoxypropyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT 2,3-EPOXYPROPYL-ALPHA-D- ...1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT 2,3-EPOXYPROPYL-ALPHA-D-GLUCOPYRANOSIDE (EPG): THE LIGAND WAS A MIXTURE OF TWO DIASTEREOISOMERS EPIMERIC AT THE 2 POSITION. I.E. 2R,S-2,3-EPOXYPROPYL ALPHA-D-GLUCOPYRANOSIDE. THIS WAS SOAKED INTO CRYSTALS AT 10 MM FOR 24 HOURS. ONLY THE R DIASTEREOISOMER REACTS WITH THE PROTEIN GIVING A COVALENT LINK TO ATOM OE2 OF GLU 184. THE RESULTANT COMPLEX IS 2S-2-HYDROXY-3-ALPHA-D-GLUCOPYRANOSYLOXY PROPOXY-GAMMA-CARBONYL-GLU184
Sequence detailsPROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ...PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ENTRY P16098. THESE CHANGES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS.

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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: 1.11→33.69 Å / Num. obs: 135507 / % possible obs: 96.3 % / Observed criterion σ(I): -9 / Redundancy: 5.98 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.56
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.76 / % possible all: 79.5

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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
Resolution: 1.2→33.168 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.833 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1407 6823 5.08 %RANDOM
Rwork0.1167 ---
obs0.118 135435 95.922 %-
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: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.243 Å20 Å20 Å2
2--0.288 Å2-0 Å2
3----0.045 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 32 729 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9525882
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73624.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23215711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5651529
X-RAY DIFFRACTIONr_chiral_restr0.1090.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214915
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_other0.1610.233
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_it1.6191.52572
X-RAY DIFFRACTIONr_mcbond_other0.7741.51039
X-RAY DIFFRACTIONr_mcangle_it2.37924171
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.10531732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2084.51678
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.52237281
X-RAY DIFFRACTIONr_sphericity_free9.673729
X-RAY DIFFRACTIONr_sphericity_bonded4.38637138
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 338 -
Rwork0.22 6814 -
obs--69.289 %

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