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- PDB-7xbs: Crystal structure of the adenylation domain of CmnG -

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Basic information

Entry
Database: PDB / ID: 7xbs
TitleCrystal structure of the adenylation domain of CmnG
ComponentsCmnG
KeywordsBIOSYNTHETIC PROTEIN / Adenylation
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
ANL, C-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...ANL, C-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsChen, I.H. / Wang, Y.L. / Chang, C.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49-026-MY3 Taiwan
CitationJournal: Chembiochem / Year: 2022
Title: Characterization and Structural Determination of CmnG-A, the Adenylation Domain That Activates the Nonproteinogenic Amino Acid Capreomycidine in Capreomycin Biosynthesis.
Authors: Chen, I.H. / Cheng, T. / Wang, Y.L. / Huang, S.J. / Hsiao, Y.H. / Lai, Y.T. / Toh, S.I. / Chu, J. / Rudolf, J.D. / Chang, C.Y.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CmnG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3652
Polymers56,2421
Non-polymers1221
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.410, 77.410, 191.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CmnG


Mass: 56242.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6YEH8
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG-400, and 100 mM CHES/Sodium hydroxide, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 72342 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 12.61 Å2 / CC1/2: 0.98 / Net I/σ(I): 38.24
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4 / Num. unique obs: 7125 / CC1/2: 0.916 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA3

4ea3


Resolution: 1.64→27.37 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 3609 4.99 %RANDOM
Rwork0.2047 68660 --
obs0.2059 72269 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.82 Å2 / Biso mean: 24.792 Å2 / Biso min: 4.49 Å2
Refinement stepCycle: final / Resolution: 1.64→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 8 275 4026
Biso mean--20.09 23.22 -
Num. residues----484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.660.27151410.242598100
1.66-1.680.25811370.2292605100
1.68-1.710.23611490.2242583100
1.71-1.730.28241270.2242598100
1.73-1.760.25211340.22822604100
1.76-1.790.26411360.22742604100
1.79-1.820.25521370.23752594100
1.82-1.850.25121420.22942611100
1.85-1.890.25371360.2232633100
1.89-1.930.22161280.21642592100
1.93-1.970.22241290.22172628100
1.97-2.010.24861300.20862603100
2.01-2.070.2391270.21452639100
2.07-2.120.24861590.21052592100
2.12-2.180.25821430.21022631100
2.18-2.250.23131570.20412596100
2.25-2.330.20131270.20072656100
2.33-2.430.2211340.20082666100
2.43-2.540.21581410.20452610100
2.54-2.670.22651470.20282664100
2.67-2.840.25461380.20192655100
2.84-3.060.21791400.20822669100
3.06-3.370.21871440.20122684100
3.37-3.850.19461480.18642711100
3.85-4.850.19551500.16922736100
4.85-27.370.23241280.2062289899
Refinement TLS params.Method: refined / Origin x: -7.9772 Å / Origin y: 22.9442 Å / Origin z: 16.5523 Å
111213212223313233
T0.1648 Å20.0276 Å2-0.0354 Å2-0.0359 Å20.0037 Å2--0.0769 Å2
L0.1241 °2-0.0698 °20.0139 °2-0.0871 °2-0.0416 °2--0.0738 °2
S0.0845 Å °0.05 Å °-0.0793 Å °-0.1579 Å °-0.0247 Å °0.0513 Å °0.0474 Å °-0.006 Å °0.1832 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 488
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB1 - 276

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