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- PDB-1b90: BACILLUS CEREUS BETA-AMYLASE APO FORM -

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Basic information

Entry
Database: PDB / ID: 1b90
TitleBACILLUS CEREUS BETA-AMYLASE APO FORM
ComponentsPROTEIN (BETA-AMYLASE)
KeywordsHYDROLASE / HYDROLASE(O-GLYCOSYL)
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
ACETATE ION / Beta-amylase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsMikami, B. / Adachi, M. / Kage, T. / Sarikaya, E. / Nanmori, T. / Shinke, R. / Utsumi, S.
CitationJournal: Biochemistry / Year: 1999
Title: Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
Authors: Mikami, B. / Adachi, M. / Kage, T. / Sarikaya, E. / Nanmori, T. / Shinke, R. / Utsumi, S.
History
DepositionMar 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BETA-AMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5544
Polymers58,3591
Non-polymers1953
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.075, 92.103, 65.671
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (BETA-AMYLASE)


Mass: 58358.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P36924, beta-amylase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.06 Å3/Da / Density % sol: 57 %
Crystal growpH: 4.6
Details: HANGING DROP VAPOR DIFFUSION AGAINST 0.1 M ACETATE BUFFER PH 4.6, 18% PEG 6000 AND 5% SATN. AMMONIUM SULFATE WITH A PROTEIN CONCENTRATION OF 10MG/ML.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Macetate1drop
318 %PEG60001reservoirprecipitant
45 %satammonium sulfate1reservoirprecipitant
50.1 Macetate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 1, 1997
RadiationMonochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 24292 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 2.47 % / Rsym value: 0.073
Reflection shellResolution: 2.449→2.578 Å / % possible all: 90
Reflection
*PLUS
Num. measured all: 59931 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→10 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -10 %RANDOM
Rwork0.164 ---
obs-20851 84.7 %-
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å22.293 Å2
2---2.94 Å20 Å2
3---0.019 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 10 120 4249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.343 -6.75 %
Rwork0.228 1632 -
obs--63.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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