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- PDB-6tp1: Crystal structure of Bacillus paralicheniformis alpha-amylase in ... -

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Basic information

Entry
Database: PDB / ID: 6tp1
TitleCrystal structure of Bacillus paralicheniformis alpha-amylase in complex with maltotetraose
ComponentsAmylase
KeywordsHYDROLASE / amylase / starch binding site
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
alpha-maltotetraose / ACETIC ACID / 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)56,3299
Polymers55,3141
Non-polymers1,0158
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-22 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.080, 82.080, 186.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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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) / Strain (production host): NEB10beta / References: UniProt: I3P686, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
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

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Non-polymers , 5 types, 376 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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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 / pH: 6 / Details: 42 - 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 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→49.26 Å / Num. obs: 48251 / % possible obs: 98.6 % / Redundancy: 8 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.071 / Rrim(I) all: 0.203 / Net I/σ(I): 8.3
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.958 / Num. unique obs: 2575 / CC1/2: 0.623 / Rpim(I) all: 0.378 / Rrim(I) all: 1.033 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimless0.5.27data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6TOY

6toy


Resolution: 1.94→49.26 Å / Cor.coef. Fo:Fc: 0.951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.201 --RANDOM
Rwork0.1866 ---
obs0.1866 48160 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.43 Å2 / Biso mean: 22.79 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: final / Resolution: 1.94→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 64 369 4343
Biso mean--36.59 31.3 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124107
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6515585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06322.634243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33215620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.411522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023274
LS refinement shellResolution: 1.94→1.987 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.304 3375 -
obs--96.79 %

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