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- PDB-8zrz: The 1.26 angstrom resolution structure of Bacillus cereus beta-am... -

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Basic information

Entry
Database: PDB / ID: 8zrz
TitleThe 1.26 angstrom resolution structure of Bacillus cereus beta-amylase in complex with maltose
ComponentsBeta-amylase
KeywordsHYDROLASE / Beta-amylase / Complex with maltose / Bacillus cereus / digestion of starch granule
Function / homology
Function and homology information


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. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / 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 / Beta-amylase active site 2. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-maltose / beta-maltose / beta-D-glucopyranose / Beta-amylase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMikami, B. / Hirata, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K05441 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural insight into sugar-binding modes of microbial ss-amylase.
Authors: Hirata, A. / Mikami, B.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)61,44717
Polymers58,3591
Non-polymers3,08916
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.974, 89.843, 66.035
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-amylase / 1 / 4-alpha-D-glucan maltohydrolase


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

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Sugars , 4 types, 6 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
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
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 877 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.39 % / Description: THICK PLATE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP VAPOR DIFFUSION AGAINST 0.1 M PHOSPHATE BUFFER PH 6.5, 15% PEG 6000 AND 5% SATN. AMMONIUM SULFATE WITH A PROTEIN CONCENTRATION OF 15MG/ML.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 171593 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Net I/σ(I): 48.5
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 7029 / CC1/2: 0.946 / Rrim(I) all: 0.246 / % possible all: 80.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660phasing
SHELXL-972018/3refinement
HKL-2000v718data reduction
HKL-2000v718data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1645 8573 5 %RANDOM
Rwork0.124 ---
obs-162442 93.4 %-
Refine analyzeNum. disordered residues: 69 / Occupancy sum non hydrogen: 5150.4
Refinement stepCycle: LAST / Resolution: 1.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4371 0 222 887 5480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0143
X-RAY DIFFRACTIONs_angle_d0.0318
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.38
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0472
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0481
X-RAY DIFFRACTIONs_approx_iso_adps0.1605

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