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- PDB-7yn1: Crystal structure of selenomethionine labeled CcbD -

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Basic information

Entry
Database: PDB / ID: 7yn1
TitleCrystal structure of selenomethionine labeled CcbD
ComponentsCcbD
KeywordsLYASE / lincomycin / celesticetin / amide bond forming enzyme
Function / homologyCcbD
Function and homology information
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMori, T. / Kadlcik, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of selenomethionine labeled CcbD
Authors: Mori, T. / Kadlcik, S. / Abe, I.
History
DepositionJul 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CcbD
B: CcbD
C: CcbD
D: CcbD


Theoretical massNumber of molelcules
Total (without water)164,3514
Polymers164,3514
Non-polymers00
Water3,315184
1
A: CcbD
C: CcbD


Theoretical massNumber of molelcules
Total (without water)82,1752
Polymers82,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-33 kcal/mol
Surface area26990 Å2
MethodPISA
2
B: CcbD

D: CcbD


Theoretical massNumber of molelcules
Total (without water)82,1752
Polymers82,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area5710 Å2
ΔGint-32 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.683, 90.932, 98.563
Angle α, β, γ (deg.)90.273, 103.671, 90.194
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
CcbD


Mass: 41087.648 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.81 Å3/Da / Density % sol: 56.24 %
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: 0.9788 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→47.88 Å / Num. obs: 60701 / % possible obs: 98.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 43.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4419 / CC1/2: 0.935 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→26.13 Å / SU ML: 0.3058 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 26.7278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 1996 3.29 %
Rwork0.2031 58633 -
obs0.2043 60629 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10742 0 0 184 10926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210994
X-RAY DIFFRACTIONf_angle_d0.523114969
X-RAY DIFFRACTIONf_chiral_restr0.0361642
X-RAY DIFFRACTIONf_plane_restr0.0041969
X-RAY DIFFRACTIONf_dihedral_angle_d16.56584001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.31561350.27124110X-RAY DIFFRACTION98.38
2.56-2.630.30271370.25434234X-RAY DIFFRACTION97.65
2.63-2.710.29361380.2544109X-RAY DIFFRACTION98.65
2.71-2.80.3251520.26654169X-RAY DIFFRACTION98.12
2.8-2.90.32841460.25514176X-RAY DIFFRACTION98.56
2.9-3.010.32151420.24414190X-RAY DIFFRACTION98.57
3.01-3.150.30611490.23894191X-RAY DIFFRACTION98.7
3.15-3.310.28311440.23664199X-RAY DIFFRACTION98.64
3.31-3.520.22651380.21724203X-RAY DIFFRACTION98.77
3.52-3.790.2271330.19484209X-RAY DIFFRACTION99.09
3.79-4.170.2321390.18954193X-RAY DIFFRACTION99.36
4.17-4.770.20091450.1674250X-RAY DIFFRACTION99.19
4.77-60.23161440.18184180X-RAY DIFFRACTION99.54
6-26.130.16111540.15674220X-RAY DIFFRACTION99.12

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