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- PDB-9uay: Crystal structure of CmnI -

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Basic information

Entry
Database: PDB / ID: 9uay
TitleCrystal structure of CmnI
ComponentsCmnI
KeywordsTRANSFERASE
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / cytoplasm
Similarity search - Function
Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL / DI(HYDROXYETHYL)ETHER / CmnI
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHsiao, P.Y. / Chang, C.Y. / Peng, C.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Org.Lett. / Year: 2025
Title: Biosynthesis of Antituberculosis Antibiotic Capreomycin Involves a trans -Iterative Adenylation Domain within the Nonribosomal Peptide Synthetase Machinery.
Authors: Lai, Y.T. / Peng, C.Y. / Liao, H.T. / Hsiao, P.Y. / Hsieh, C.K. / Luo, Y.R. / Huang, S.C. / Wang, Y.L. / Ma, T. / Chen, Y.R. / Kuo, Y.M. / Lin, Y.C. / Chu, J. / Chang, C.Y.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CmnI
B: CmnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,52911
Polymers123,1372
Non-polymers1,3929
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint23 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.888, 129.520, 61.313
Angle α, β, γ (deg.)90.00, 95.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CmnI


Mass: 61568.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6YEI0

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H26O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 1000 100 mM Tris base/ Hydrochloric acid pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→27.65 Å / Num. obs: 61605 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rsym value: 0.056 / Net I/σ(I): 20.8
Reflection shellResolution: 2.17→2.25 Å / Num. unique obs: 6681 / Rsym value: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.17→27.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.956 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24552 3301 5.1 %RANDOM
Rwork0.2149 ---
obs0.21644 61605 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.3 Å2
2--0.67 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.17→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 102 130 6858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126885
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166653
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.8259380
X-RAY DIFFRACTIONr_angle_other_deg0.4711.75815182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.722598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.859101016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021669
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5723.6433397
X-RAY DIFFRACTIONr_mcbond_other2.5723.6433397
X-RAY DIFFRACTIONr_mcangle_it4.2326.5394242
X-RAY DIFFRACTIONr_mcangle_other4.2326.544243
X-RAY DIFFRACTIONr_scbond_it2.8234.0293488
X-RAY DIFFRACTIONr_scbond_other2.8234.0313489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7527.1975137
X-RAY DIFFRACTIONr_long_range_B_refined8.89958.017253
X-RAY DIFFRACTIONr_long_range_B_other8.97158.267239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.172→2.228 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 166 -
Rwork0.299 3104 -
obs--64.73 %

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