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- PDB-1ven: Crystal Structure Analysis of Y164E/maltose of Bacilus cereus Bet... -

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Basic information

Entry
Database: PDB / ID: 1ven
TitleCrystal Structure Analysis of Y164E/maltose of Bacilus cereus Beta-amylase at pH 4.6
ComponentsBeta-amylase
KeywordsHYDROLASE / beta-alpha-barrels / optimum pH / Y164E
Function / homology
Function and homology information


amylopectin maltohydrolase activity / beta-amylase / beta-amylase activity / starch binding / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Beta-amylase active site 1. / Glycoside hydrolase, family 14, conserved site / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14 / Starch binding domain / Carbohydrate binding module family 20 / CBM20 (carbohydrate binding type-20) domain profile. ...Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Beta-amylase active site 1. / Glycoside hydrolase, family 14, conserved site / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14 / Starch binding domain / Carbohydrate binding module family 20 / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Beta-amylase
Similarity search - Component
Biological speciesBacillus cereus (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHirata, A. / Adachi, M. / Utsumi, S. / Mikami, B.
CitationJournal: Biochemistry / Year: 2004
Title: Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type
Authors: Hirata, A. / Adachi, M. / Utsumi, S. / Mikami, B.
History
DepositionApr 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)58,7254
Polymers58,3241
Non-polymers4003
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.489, 92.899, 65.962
Angle α, β, γ (deg.)90.00, 102.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-amylase / / 1 / 4-alpha-D-glucan maltohydrolase / Glycoside Hydrolase Family 14


Mass: 58324.461 Da / Num. of mol.: 1 / Mutation: Y164E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (unknown) / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P36924, beta-amylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 6000, ammonium sulfate, potassium phosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 29, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30.5 Å / Num. all: 48233 / Num. obs: 48233 / % possible obs: 87.2 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 7.7 Å2
Reflection shellResolution: 1.87→1.94 Å / Num. unique all: 2257 / % possible all: 34.6

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Processing

Software
NameVersionClassification
CNS1refinement
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9Z
Resolution: 2.02→14.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 730672.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3750 10.1 %RANDOM
Rwork0.193 ---
obs0.193 37221 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2698 Å2 / ksol: 0.319965 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å2-3.65 Å2
2--7.92 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.02→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 24 262 4447
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 469 10.1 %
Rwork0.326 4197 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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