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- PDB-8h8i: Triterpenoid saponin acetyltransferase, AmAT7-3 -

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Basic information

Entry
Database: PDB / ID: 8h8i
TitleTriterpenoid saponin acetyltransferase, AmAT7-3
ComponentsAmAT7-3
KeywordsBIOSYNTHETIC PROTEIN / Acstyltransferase / Triterpene saponin
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: 2.03 Å
AuthorsWang, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
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 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7732
Polymers49,9881
Non-polymers7851
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.630, 135.630, 192.180
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-654-

HOH

21A-742-

HOH

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Components

#1: Protein AmAT7-3


Mass: 49988.496 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Nonpolymer detailsThe CAS number of KZO is 83207-58-3.

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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 / pH: 6.19
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: BL17U1 / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.03→74.37 Å / Num. obs: 43854 / % possible obs: 99.6 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 14
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 0.046 / Num. unique obs: 3190 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
PHENIX1.16refinement
Coot7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KEC

4kec


Resolution: 2.03→44.469 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 2179 4.98 %
Rwork0.2092 --
obs0.211 43743 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→44.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 55 161 3568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083488
X-RAY DIFFRACTIONf_angle_d0.9264765
X-RAY DIFFRACTIONf_dihedral_angle_d5.9912072
X-RAY DIFFRACTIONf_chiral_restr0.055558
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.07420.42731290.40032451X-RAY DIFFRACTION96
2.1224-2.17550.30211320.29342572X-RAY DIFFRACTION100
2.1755-2.23430.29531280.29042576X-RAY DIFFRACTION99
2.2343-2.30.41841390.30792581X-RAY DIFFRACTION99
2.3-2.37430.30831350.24012573X-RAY DIFFRACTION100
2.3743-2.45910.26781390.23252602X-RAY DIFFRACTION100
2.4591-2.55760.27411410.22912575X-RAY DIFFRACTION100
2.5576-2.6740.27151400.22022592X-RAY DIFFRACTION100
2.674-2.81490.26751460.20992594X-RAY DIFFRACTION100
2.8149-2.99130.24381300.21862603X-RAY DIFFRACTION100
2.9913-3.22220.24681530.20642592X-RAY DIFFRACTION100
3.2222-3.54630.25261340.19372621X-RAY DIFFRACTION100
3.5463-4.05910.22671300.18532663X-RAY DIFFRACTION100
4.0591-5.11290.19241180.17362667X-RAY DIFFRACTION100

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