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- PDB-2xfy: Crystal structure of Barley Beta-Amylase complexed with alpha- cy... -

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Basic information

Entry
Database: PDB / ID: 2xfy
TitleCrystal structure of Barley Beta-Amylase complexed with alpha- cyclodextrin
ComponentsBETA-AMYLASE
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / 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
alpha-cyclodextrin / Beta-amylase
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.207 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.M. / Southard, A.M. / Stanley, D. / Denyer, K. / Smith, A.M. / Naldrett, M.J. / Lawson, D.M. / Field, R.A.
History
DepositionMay 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_symm_contact / 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_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_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 / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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)60,7854
Polymers59,6701
Non-polymers1,1153
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.846, 71.466, 92.472
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: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT ALPHA-CYCLODEXTRIN (CYCLOHEXA- ...1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE) (ACX): SOAKED INTO CRYSTALS AT 10 MM FOR 24 HOURS
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. AUTHOR SUGGESTS THESE ARE NATURAL VARIANTS

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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: Diamond / Beamline: I02 / Wavelength: 0.9507
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 1.19→28.09 Å / Num. obs: 139370 / % possible obs: 98.4 % / Observed criterion σ(I): -9 / Redundancy: 5.19 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.31
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.46 / % possible all: 90.8

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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: 1.207→25.76 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.05 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1533 6970 5.06 %RANDOM
Rwork0.1221 ---
obs0.124 138417 98.783 %-
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: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.096 Å20 Å20 Å2
2--0.199 Å20 Å2
3----0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.207→25.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 74 817 4775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9656120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37524.034233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0281532
X-RAY DIFFRACTIONr_chiral_restr0.110.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215059
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_other0.1680.244
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_it1.6251.52601
X-RAY DIFFRACTIONr_mcbond_other0.7471.51044
X-RAY DIFFRACTIONr_mcangle_it2.37524241
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.15231850
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3714.51831
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.51737540
X-RAY DIFFRACTIONr_sphericity_free8.8173817
X-RAY DIFFRACTIONr_sphericity_bonded3.9937370
LS refinement shellResolution: 1.207→1.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 499 -
Rwork0.27 9134 -
obs--94.091 %

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