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- PDB-8cqf: Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromo... -

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Basic information

Entry
Database: PDB / ID: 8cqf
TitleCrystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Complexed with Rearranged Acarbose
ComponentsAlpha-amylase
KeywordsHYDROLASE / Inhibitor / Alpha-Amylase / Chimeric
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSkagseth, S. / Griese, J.J. / Lund, B.A. / van der Ent, F. / Aqvist, J.
Funding support Sweden, Norway, 4items
OrganizationGrant numberCountry
Swedish Research Council2018-04170 Sweden
Swedish Research Council2022-03441 Sweden
Research Council of Norway262695 Norway
Research Council of Norway274858 Norway
CitationJournal: Sci Adv / Year: 2023
Title: Computational design of the temperature optimum of an enzyme reaction.
Authors: van der Ent, F. / Skagseth, S. / Lund, B.A. / Socan, J. / Griese, J.J. / Brandsdal, B.O. / Aqvist, J.
History
DepositionMar 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9649
Polymers49,2251
Non-polymers2,7398
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-16 kcal/mol
Surface area16590 Å2
Unit cell
Length a, b, c (Å)68.597, 81.071, 129.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 49224.996 Da / Num. of mol.: 1
Mutation: A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Gene: amy / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P29957, alpha-amylase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-1,5-anhydro-D-glucitol


Type: oligosaccharide / Mass: 467.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h2122h_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 807.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122m-1a_1-5]/1-2-1-1/a4-b1_b4n2-c1n1*1OC^RC^RC^SC^SN*2/6C=^ZCCO/10$3/5O/4O_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 301 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3 M NaCl, 0.1 M BisTris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→38.69 Å / Num. obs: 84778 / % possible obs: 96.7 % / Redundancy: 2.9 % / CC1/2: 0.993 / Net I/σ(I): 6.5
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 25013 / CC1/2: 0.471

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→38.69 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 2077 2.45 %
Rwork0.1687 --
obs0.1694 84778 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 182 297 3938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013764
X-RAY DIFFRACTIONf_angle_d1.2045140
X-RAY DIFFRACTIONf_dihedral_angle_d8.018504
X-RAY DIFFRACTIONf_chiral_restr0.078580
X-RAY DIFFRACTIONf_plane_restr0.015650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.36681390.29485520X-RAY DIFFRACTION96
2.1-2.150.31631400.27685669X-RAY DIFFRACTION99
2.15-2.210.26291420.24275699X-RAY DIFFRACTION99
2.21-2.270.2471430.24245622X-RAY DIFFRACTION99
2.27-2.340.30341410.22195636X-RAY DIFFRACTION99
2.34-2.430.2481460.20795660X-RAY DIFFRACTION99
2.43-2.520.23691430.20425601X-RAY DIFFRACTION98
2.52-2.640.2691360.1925563X-RAY DIFFRACTION97
2.64-2.780.21891380.18935537X-RAY DIFFRACTION96
2.78-2.950.2271340.18125200X-RAY DIFFRACTION91
2.95-3.180.19641330.16345305X-RAY DIFFRACTION93
3.18-3.50.17131360.15685505X-RAY DIFFRACTION97
3.5-4.010.14591420.12075479X-RAY DIFFRACTION96
4.01-5.050.15631340.11615402X-RAY DIFFRACTION94
5.05-38.690.15171300.15955303X-RAY DIFFRACTION93

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