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- PDB-7yn2: Crystal structure of CcbD with methylthiolincosamide -

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Basic information

Entry
Database: PDB / ID: 7yn2
TitleCrystal structure of CcbD with methylthiolincosamide
ComponentsCcbD
KeywordsLYASE / lincomycin / celesticetin / amide bond forming enzyme
Function / homologyChem-IYV / CcbD
Function and homology information
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMori, T. / Lyu, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of CcbD with methylthiolincosamide
Authors: Mori, T. / Lyu, S. / Abe, I.
History
DepositionJul 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CcbD
B: CcbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9553
Polymers80,7012
Non-polymers2531
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-34 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.059, 52.903, 90.938
Angle α, β, γ (deg.)90.000, 91.103, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein CcbD


Mass: 40350.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002772 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES9
#2: Chemical ChemComp-IYV / (2R,3R,4S,5R,6R)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-6-methylsulfanyl-oxane-3,4,5-triol


Mass: 253.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Tris-HCl (pH 6.7), 0.16 M magnesium chloride, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→48.01 Å / Num. obs: 40659 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3958 / CC1/2: 0.919 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YN1

7yn1


Resolution: 2.3→48.01 Å / SU ML: 0.2552 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 2028 4.99 %
Rwork0.1995 38609 -
obs0.2014 40637 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5341 0 16 258 5615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825483
X-RAY DIFFRACTIONf_angle_d0.93837471
X-RAY DIFFRACTIONf_chiral_restr0.0501826
X-RAY DIFFRACTIONf_plane_restr0.0097980
X-RAY DIFFRACTIONf_dihedral_angle_d16.40862006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31481630.25312704X-RAY DIFFRACTION99.83
2.36-2.420.29751460.23792683X-RAY DIFFRACTION97.28
2.42-2.490.29311380.24282760X-RAY DIFFRACTION99.31
2.49-2.570.28241650.22982683X-RAY DIFFRACTION98.21
2.57-2.660.29371580.22822699X-RAY DIFFRACTION98.11
2.66-2.770.26371450.23022784X-RAY DIFFRACTION99.29
2.77-2.90.22691450.22532728X-RAY DIFFRACTION99.38
2.9-3.050.30821440.2322729X-RAY DIFFRACTION98.86
3.05-3.240.28651440.23112754X-RAY DIFFRACTION98.87
3.24-3.490.29291470.22282759X-RAY DIFFRACTION99.25
3.49-3.840.23861150.20452786X-RAY DIFFRACTION99.18
3.84-4.40.2151380.1792814X-RAY DIFFRACTION99.76
4.4-5.540.21151380.16022823X-RAY DIFFRACTION99.6
5.54-48.010.1371420.15662903X-RAY DIFFRACTION99.44

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