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- PDB-1b9z: BACILLUS CEREUS BETA-AMYLASE COMPLEXED WITH MALTOSE -

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Basic information

Entry
Database: PDB / ID: 1b9z
TitleBACILLUS CEREUS BETA-AMYLASE COMPLEXED WITH MALTOSE
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. / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14, conserved site / Glycoside hydrolase, family 14 / Starch binding domain / Carbohydrate binding module family 20 / Starch binding domain ...Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Beta-amylase active site 1. / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14, conserved site / Glycoside hydrolase, family 14 / Starch binding domain / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Beta-amylase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 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
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_chiral / struct_conn / struct_conn_type / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9238
Polymers58,3591
Non-polymers1,5647
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)58.160, 93.740, 66.660
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules A

#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: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 278 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


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


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


Mass: 18.015 Da / Num. of mol.: 275 / 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: Mar 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→30 Å / Num. obs: 39463 / % possible obs: 83.4 % / Observed criterion σ(I): 1 / Redundancy: 2.33 % / Rsym value: 0.046
Reflection shellResolution: 1.999→2.07 Å / % possible all: 38.7
Reflection
*PLUS
Num. measured all: 92118 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 38.7 %

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
PHASESphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→11 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -10 %RANDOM
Rwork0.17 ---
obs-33365 82.3 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-5.667 Å20 Å20.993 Å2
2---5.99 Å20 Å2
3---0.327 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.1→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 102 275 4496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.07
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.06
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: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.292 -5.95 %
Rwork0.242 2773 -
obs--60.86 %
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_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.06

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