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- PDB-8hbt: AmAT7-3 mutant A310G -

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Basic information

Entry
Database: PDB / ID: 8hbt
TitleAmAT7-3 mutant A310G
ComponentsAmAT7-3-A310G
KeywordsBIOSYNTHETIC PROTEIN / Acetyltransferase / Triterpene saponin / Mutant
Function / homologyChloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 2-Layer Sandwich / Alpha Beta / Astragaloside IV
Function and homology information
Biological speciesAstragalus membranaceus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWang, L.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus.
Authors: Wang, L. / Jiang, Z. / Zhang, J. / Chen, K. / Zhang, M. / Wang, Z. / Wang, B. / Ye, M. / Qiao, X.
History
DepositionOct 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmAT7-3-A310G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7592
Polymers49,9741
Non-polymers7851
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18740 Å2
Unit cell
Length a, b, c (Å)136.020, 136.020, 192.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

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Components

#1: Protein AmAT7-3-A310G


Mass: 49974.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Astragalus membranaceus (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-KZO / Astragaloside IV


Mass: 784.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H68O14 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.6 M magnesium sulfate, 100 Mm MES/sodium hydroxide pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→36.53 Å / Num. obs: 49037 / % possible obs: 99.7 % / Redundancy: 19 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 16.4
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 3426 / Rsym value: 0.032

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
PDB_EXTRACT3.27data extraction
Coot7.1model building
PHENIX1.16_3549phasing
Aimless0.7.7data scaling
HKL-2000HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H8I

8h8i


Resolution: 1.96→36.53 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 2397 4.89 %
Rwork0.2062 --
obs0.2073 48995 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 55 181 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073537
X-RAY DIFFRACTIONf_angle_d0.8624826
X-RAY DIFFRACTIONf_dihedral_angle_d6.1092111
X-RAY DIFFRACTIONf_chiral_restr0.056558
X-RAY DIFFRACTIONf_plane_restr0.005609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9601-2.00010.4341410.41492737X-RAY DIFFRACTION99
2.0435-2.09110.40391440.32422718X-RAY DIFFRACTION99
2.0911-2.14340.29461150.29132723X-RAY DIFFRACTION100
2.1434-2.20130.28991390.26852735X-RAY DIFFRACTION99
2.2013-2.26610.28011330.24082713X-RAY DIFFRACTION100
2.2661-2.33920.26621400.22182708X-RAY DIFFRACTION100
2.3392-2.42280.28361290.22692731X-RAY DIFFRACTION100
2.4228-2.51980.24991350.22842730X-RAY DIFFRACTION100
2.5198-2.63440.28071650.22752690X-RAY DIFFRACTION100
2.6344-2.77330.26021330.20982764X-RAY DIFFRACTION100
2.7733-2.9470.24671420.22152740X-RAY DIFFRACTION100
2.947-3.17440.24261340.2152749X-RAY DIFFRACTION100
3.1744-3.49360.22761340.19992781X-RAY DIFFRACTION100
3.9986-5.03570.18451340.16572803X-RAY DIFFRACTION100

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