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- PDB-9upq: Structure of 3-amino-3-carboxyltransferase -

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Basic information

Entry
Database: PDB / ID: 9upq
TitleStructure of 3-amino-3-carboxyltransferase
ComponentsIsonocardicin synthase
KeywordsTRANSFERASE / 3-amino-3-carboxyltransferase / nocardicin / biosynthesis
Function / homologyisonocardicin synthase / isonocardicin synthase activity / Methyltransferase domain 25 / Methyltransferase domain / antibiotic biosynthetic process / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Isonocardicin synthase
Function and homology information
Biological speciesNocardia uniformis subsp. tsuyamanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGao, Y. / Mori, T. / Awakawa, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Basis for 3-Amino-3-carboxypropyl Transfer in Nocardicin Biosynthesis.
Authors: Gao, Y. / Karasawa, M. / Quan, Z. / Mori, T. / Kanaida, M. / Townsend, C.A. / Terada, T. / Abe, I. / Awakawa, T.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: 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)71,0713
Polymers71,0362
Non-polymers351
Water7,981443
1
A: Isonocardicin synthase
hetero molecules

B: Isonocardicin synthase


Theoretical massNumber of molelcules
Total (without water)71,0713
Polymers71,0362
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1620 Å2
ΔGint-16 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.710, 91.874, 130.790
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 200 mM Ammonium nitrate pH6.3

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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: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.75→46.71 Å / Num. obs: 57752 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3146 / CC1/2: 0.741 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.75→45.94 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 2000 3.47 %
Rwork0.1765 55674 -
obs0.1781 57674 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 1 443 4802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724494
X-RAY DIFFRACTIONf_angle_d0.97436111
X-RAY DIFFRACTIONf_chiral_restr0.0595684
X-RAY DIFFRACTIONf_plane_restr0.0108820
X-RAY DIFFRACTIONf_dihedral_angle_d5.9591648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.33031420.24883940X-RAY DIFFRACTION99.95
1.79-1.840.26931400.22193909X-RAY DIFFRACTION100
1.84-1.90.26411400.2153909X-RAY DIFFRACTION100
1.9-1.960.21341420.19133942X-RAY DIFFRACTION100
1.96-2.030.21331410.18343926X-RAY DIFFRACTION100
2.03-2.110.2321420.18173948X-RAY DIFFRACTION100
2.11-2.20.24251410.18113923X-RAY DIFFRACTION100
2.2-2.320.23651420.18063947X-RAY DIFFRACTION100
2.32-2.470.22571420.18333974X-RAY DIFFRACTION100
2.47-2.660.23471430.18173947X-RAY DIFFRACTION99.95
2.66-2.920.24181430.18144009X-RAY DIFFRACTION99.95
2.92-3.350.21341440.17614012X-RAY DIFFRACTION100
3.35-4.220.19281460.15224057X-RAY DIFFRACTION100
4.22-45.940.20881520.1664231X-RAY DIFFRACTION99.95

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