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- PDB-6toy: Crystal structure of Bacillus paralicheniformis wild-type alpha-a... -

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Basic information

Entry
Database: PDB / ID: 6toy
TitleCrystal structure of Bacillus paralicheniformis wild-type alpha-amylase
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
ACETIC ACID / FORMIC ACID / MALONATE ION / Amylase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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

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Assembly

Deposited unit
A: Amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,76810
Polymers55,3141
Non-polymers4549
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-36 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.500, 83.500, 188.510
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 , 1 types, 1 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): NEB10 beta / References: UniProt: I3P686, alpha-amylase

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Non-polymers , 6 types, 447 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 59 %
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: Oct 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→47.13 Å / Num. obs: 49554 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.05 / Rrim(I) all: 0.135 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.828 / Num. unique obs: 3415 / CC1/2: 0.605 / Rpim(I) all: 0.328 / Rrim(I) all: 0.894 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.4 Å47.13 Å
Translation7.4 Å47.13 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLI

1bli


Resolution: 1.95→47.13 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.422 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 2431 4.9 %RANDOM
Rwork0.1698 ---
obs0.1715 47044 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.37 Å2 / Biso mean: 26.481 Å2 / Biso min: 15.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.95→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 26 438 4374
Biso mean--42.01 34.74 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194074
X-RAY DIFFRACTIONr_bond_other_d0.0020.023473
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9045533
X-RAY DIFFRACTIONr_angle_other_deg0.97538045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91923.919222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 176 -
Rwork0.259 3422 -
all-3598 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.9 Å / Origin y: -32.398 Å / Origin z: 16.999 Å
111213212223313233
T0.0345 Å20.0103 Å20.0062 Å2-0.1165 Å20.0397 Å2--0.038 Å2
L0.4797 °20.1494 °2-0.2237 °2-0.5891 °2-0.2796 °2--0.6324 °2
S-0.021 Å °0.0205 Å °-0.0656 Å °0.0066 Å °-0.0231 Å °0.0448 Å °0.0457 Å °0.0342 Å °0.0442 Å °

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