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- PDB-1cqy: STARCH BINDING DOMAIN OF BACILLUS CEREUS BETA-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1cqy
TitleSTARCH BINDING DOMAIN OF BACILLUS CEREUS BETA-AMYLASE
ComponentsBETA-AMYLASE
KeywordsHYDROLASE / STARCH-BINDING DOMAIN / B-AMYLASE / 3D STRUCTURE
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch binding / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. ...Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsYoon, H.J. / Hirata, A. / Adachi, M. / Sekine, A. / Utsumi, S. / Mikami, B.
CitationJournal: To be Published
Title: Structure of Separated Starch-Binding Domain of Bacillus cereus B-amylase
Authors: Yoon, H.J. / Hirata, A. / Adachi, M. / Sekine, A. / Utsumi, S. / Mikami, B.
History
DepositionAug 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-AMYLASE


Theoretical massNumber of molelcules
Total (without water)11,3111
Polymers11,3111
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.195, 60.195, 64.922
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-AMYLASE /


Mass: 11310.645 Da / Num. of mol.: 1 / Fragment: STARCH-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4N9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→35 Å / Num. all: 66133 / Num. obs: 10179 / % possible obs: 92.72 % / Observed criterion σ(F): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 1.84
Reflection shellResolution: 1.91→1.98 Å / Rmerge(I) obs: 0.412 / % possible all: 63.4

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
FRAMBOdata collection
SADIEdata scaling
SAINTdata scaling
X-PLORphasing
RefinementResolution: 1.95→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 854 -RANDOM
Rwork0.181 ---
obs0.181 -82.6 %-
all-8264 --
Refinement stepCycle: LAST / Resolution: 1.95→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 0 107 907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.513
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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