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- PDB-9e50: TAD from Carmabin Biosynthetic Pathway in complex with NAD - Crys... -

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Basic information

Entry
Database: PDB / ID: 9.0E+50
TitleTAD from Carmabin Biosynthetic Pathway in complex with NAD - Crystal Form 2
ComponentsAmino acid adenylation domain protein
KeywordsBIOSYNTHETIC PROTEIN / NAD-binding
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / protein-arginine N-methyltransferase activity / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / nucleotide binding / cytoplasm
Similarity search - Function
TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Methyltransferase domain / Methyltransferase domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain ...TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Methyltransferase domain / Methyltransferase domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
IODIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Amino acid adenylation domain protein
Similarity search - Component
Biological speciesMoorena producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsRankin, M.R. / Smith, J.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA265082 United States
Citation
Journal: Nat.Chem.Biol. / Year: 2025
Title: Designing small molecules targeting a cryptic RNA binding site through base displacement.
Authors: Olenginski, L.T. / Wierzba, A.J. / Laursen, S.P. / Batey, R.T.
#1: Journal: Structure / Year: 2025
Title: Structure of a putative terminal amidation domain in natural product biosynthesis.
Authors: Rankin, M.R. / Khare, D. / Gerwick, L. / Sherman, D.H. / Gerwick, W.H. / Smith, J.L.
History
DepositionOct 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 14, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Sep 24, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid adenylation domain protein
B: Amino acid adenylation domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4836
Polymers88,9022
Non-polymers1,5814
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.433, 72.813, 209.207
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 Amino acid adenylation domain protein / Putative nonribosomal peptide synthetase


Mass: 44450.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cleaved at N-terminus by TEV protease / Source: (gene. exp.) Moorena producens 3L (bacteria) / Gene: LYNGBM3L_66040 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4Y2B0
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM bis-tris propane pH 8.5, 0.1M sodium iodide, 21% PEG 3350, 3% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2023
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.68→43.16 Å / Num. obs: 96746 / % possible obs: 99.27 % / Redundancy: 7.7 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.68
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.498 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 9433 / CC1/2: 0.512 / % possible all: 98.53

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→43.16 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 23.0958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 2000 2.07 %
Rwork0.2012 94743 -
obs0.2018 96743 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.54 Å2
Refinement stepCycle: LAST / Resolution: 1.68→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 90 630 6803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346341
X-RAY DIFFRACTIONf_angle_d0.62828621
X-RAY DIFFRACTIONf_chiral_restr0.0446984
X-RAY DIFFRACTIONf_plane_restr0.0041097
X-RAY DIFFRACTIONf_dihedral_angle_d12.58452318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.48421390.43986599X-RAY DIFFRACTION98.7
1.72-1.770.40751410.38416654X-RAY DIFFRACTION98.62
1.77-1.820.32571400.31446643X-RAY DIFFRACTION98.66
1.82-1.880.29281400.26516674X-RAY DIFFRACTION99.26
1.88-1.950.25811410.2326650X-RAY DIFFRACTION98.52
1.95-2.020.26011420.22956709X-RAY DIFFRACTION99.16
2.02-2.120.27011420.23636735X-RAY DIFFRACTION99.68
2.12-2.230.25061430.22376763X-RAY DIFFRACTION99.54
2.23-2.370.26661430.20666755X-RAY DIFFRACTION99.7
2.37-2.550.24941420.20346783X-RAY DIFFRACTION99.3
2.55-2.810.22881440.20326815X-RAY DIFFRACTION99.9
2.81-3.210.21391450.19916860X-RAY DIFFRACTION99.8
3.21-4.050.21471460.17096907X-RAY DIFFRACTION99.44
4.05-43.160.17231520.16087196X-RAY DIFFRACTION99.53

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