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- PDB-6tp2: Crystal structure of Bacillus paralicheniformis alpha-amylase in ... -

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Basic information

Entry
Database: PDB / ID: 6tp2
TitleCrystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin
ComponentsAmylase
KeywordsHYDROLASE / amylase / starch binding site / cyclodextrin
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-cyclodextrin / MALONATE ION / Amylase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase.
Authors: Bozic, N. / Rozeboom, H.J. / Loncar, N. / Slavic, M.S. / Janssen, D.B. / Vujcic, Z.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6957
Polymers55,3141
Non-polymers1,3816
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-46 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.940, 82.940, 187.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Amylase


Mass: 55313.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: amy / Production host: Escherichia coli (E. coli) / Variant (production host): NEB10beta / References: UniProt: I3P686, alpha-amylase
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 424 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 41 - 46 % Tacsimate, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→46.8 Å / Num. obs: 49463 / % possible obs: 98.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 9.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.071 / Rrim(I) all: 0.197 / Net I/σ(I): 7.8
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.804 / Num. unique obs: 2544 / CC1/2: 0.609 / Rpim(I) all: 0.328 / Rrim(I) all: 0.871 / % possible all: 77.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6TOY

6toy


Resolution: 1.94→46.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.284 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.121
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2427 4.9 %RANDOM
Rwork0.1709 ---
obs0.1723 46912 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.14 Å2 / Biso mean: 21.669 Å2 / Biso min: 10.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0 Å2
2---0.18 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.94→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 88 419 4417
Biso mean--40.89 28.87 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194129
X-RAY DIFFRACTIONr_bond_other_d0.0020.023501
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9285622
X-RAY DIFFRACTIONr_angle_other_deg0.96638138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97223.937221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50215620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6211522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
LS refinement shellResolution: 1.94→1.986 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.294 173 -
Rwork0.285 3245 -
obs--95.05 %
Refinement TLS params.Method: refined / Origin x: -8.535 Å / Origin y: -32.206 Å / Origin z: 16.763 Å
111213212223313233
T0.0279 Å20.0065 Å2-0.0007 Å2-0.0652 Å20.0135 Å2--0.013 Å2
L0.417 °20.1155 °2-0.2199 °2-0.4265 °2-0.2091 °2--0.6817 °2
S-0.0318 Å °-0.0003 Å °-0.0415 Å °-0.0038 Å °-0.0088 Å °0.0216 Å °0.024 Å °0.0231 Å °0.0406 Å °

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