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- PDB-9e56: TAD from Carmabin Biosynthetic Pathway with Disulfide between Cys... -

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Basic information

Entry
Database: PDB / ID: 9.0E+56
TitleTAD from Carmabin Biosynthetic Pathway with Disulfide between Cys2238 and Dephosphocoenzyme A - 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 / phosphopantetheine 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 / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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
DEPHOSPHO COENZYME A / IODIDE ION / Amino acid adenylation domain protein
Similarity search - Component
Biological speciesMoorena producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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
CitationJournal: 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 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)90,5316
Polymers88,9022
Non-polymers1,6294
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-44 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.820, 72.867, 211.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#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.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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, 75 mM sodium iodide, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.94→43.74 Å / Num. obs: 64714 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0916 / Net I/σ(I): 11.24
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 39309 / CC1/2: 0.579 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→43.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.84 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1336 2.06 %
Rwork0.1937 --
obs0.1944 64703 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 2 392 6501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056249
X-RAY DIFFRACTIONf_angle_d0.7938488
X-RAY DIFFRACTIONf_dihedral_angle_d16.0462276
X-RAY DIFFRACTIONf_chiral_restr0.053964
X-RAY DIFFRACTIONf_plane_restr0.0041078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.010.30321340.28366224X-RAY DIFFRACTION100
2.01-2.090.3241300.27096286X-RAY DIFFRACTION100
2.09-2.180.30351300.24626247X-RAY DIFFRACTION100
2.18-2.30.27041360.22236284X-RAY DIFFRACTION100
2.3-2.440.23841340.21246279X-RAY DIFFRACTION100
2.44-2.630.27551280.21086316X-RAY DIFFRACTION100
2.63-2.90.23931340.20856315X-RAY DIFFRACTION100
2.9-3.320.22481380.20346382X-RAY DIFFRACTION100
3.32-4.180.22461320.17446383X-RAY DIFFRACTION99
4.18-43.740.18251400.16526651X-RAY DIFFRACTION99

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