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- PDB-8zhv: Structure of 3-amino-3-carboxyltransferase in complex with SAH an... -

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Basic information

Entry
Database: PDB / ID: 8zhv
TitleStructure of 3-amino-3-carboxyltransferase in complex with SAH and nocardicin G in the biosynthesis of nocardicins
ComponentsIsonocardicin synthase
KeywordsTRANSFERASE / 3-amino-3-carboxyltransferase / nocardicin / biosynthesis
Function / homology
Function and homology information


isonocardicin synthase / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / 5'-thioadenosine / S-ADENOSYL-L-HOMOCYSTEINE / Isonocardicin synthase
Similarity search - Component
Biological speciesNocardia uniformis subsp. tsuyamanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsGao, Y. / Mori, T. / Awakawa, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of 3-amino-3-carboxyltransferase in complex with SAH and nocardicin G in the biosynthesis of nocardicins
Authors: Gao, Y. / Mori, T. / Awakawa, T. / Abe, I.
History
DepositionMay 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isonocardicin synthase
B: Isonocardicin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4746
Polymers71,0362
Non-polymers1,4384
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-8 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.221, 76.582, 146.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isonocardicin synthase / Nocardicin 3-amino-3-carboxypropyltransferase


Mass: 35517.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia uniformis subsp. tsuyamanensis (bacteria)
Gene: nat, nocC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RAH6, isonocardicin synthase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1L1U / Nocardicin G / (2~{R})-2-[(3~{S})-3-[[(2~{R})-2-azanyl-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanylidene-azetidin-1-yl]-2-(4-hydroxyphenyl)ethanoic acid


Mass: 385.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N3O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A4D / 5'-thioadenosine


Mass: 283.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200 mM Ammonium nitrate pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.13→48.92 Å / Num. obs: 31289 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 26.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.1
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2544 / CC1/2: 0.768 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.13→45.81 Å / SU ML: 0.2307 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.8542
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1898 6.42 %
Rwork0.1822 27652 -
obs0.1853 29550 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.18 Å2
Refinement stepCycle: LAST / Resolution: 2.13→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 101 197 4622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724521
X-RAY DIFFRACTIONf_angle_d0.95186157
X-RAY DIFFRACTIONf_chiral_restr0.0515687
X-RAY DIFFRACTIONf_plane_restr0.0082817
X-RAY DIFFRACTIONf_dihedral_angle_d9.1106657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.28491220.22121769X-RAY DIFFRACTION85.84
2.18-2.240.27711260.21071773X-RAY DIFFRACTION87.03
2.24-2.310.2621260.20951851X-RAY DIFFRACTION89.7
2.31-2.380.26521280.19521867X-RAY DIFFRACTION91.35
2.38-2.470.32211300.19621905X-RAY DIFFRACTION92.42
2.47-2.570.29011280.19841912X-RAY DIFFRACTION92.52
2.57-2.680.26441390.18931976X-RAY DIFFRACTION95.4
2.68-2.820.23831370.18362001X-RAY DIFFRACTION96.22
2.83-30.2111360.17791978X-RAY DIFFRACTION96.35
3-3.230.21041400.16282058X-RAY DIFFRACTION98.12
3.23-3.560.17561410.16122053X-RAY DIFFRACTION98.83
3.56-4.070.19361450.16862124X-RAY DIFFRACTION99.96
4.07-5.130.23071450.17052133X-RAY DIFFRACTION99.87
5.13-45.810.2271550.19852252X-RAY DIFFRACTION99.79

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