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- PDB-7qug: Crystal structure of carbon-sulfur lyase FnaPatB1 from Fusobacter... -

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Basic information

Entry
Database: PDB / ID: 7qug
TitleCrystal structure of carbon-sulfur lyase FnaPatB1 from Fusobacterium nucleatum subspecies animalis in complex with allyl-cysteine
Componentscarbon-sulfur lyase FnaPatB1
KeywordsLYASE / carbon-sulfur lyase / PLP-dependent aminotransferase
Function / homologyACETATE ION / CACODYLATE ION / allyl-cysteine
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchwartz, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Institute of Agricultural Research (INRAE) France
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Metabolism of Cysteine Conjugates and Production of Flavor Sulfur Compounds by a Carbon-Sulfur Lyase from the Oral Anaerobe Fusobacterium nucleatum.
Authors: Neiers, F. / Gourrat, K. / Canon, F. / Schwartz, M.
History
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carbon-sulfur lyase FnaPatB1
B: carbon-sulfur lyase FnaPatB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6125
Polymers95,2552
Non-polymers3573
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-24 kcal/mol
Surface area30890 Å2
Unit cell
Length a, b, c (Å)106.049, 106.049, 204.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARG(chain 'A' and (resid 1 through 10 or resid 38 through 397))AA1 - 101 - 10
12ASPASPLYSLYS(chain 'A' and (resid 1 through 10 or resid 38 through 397))AA38 - 39738 - 397
23METMETARGARG(chain 'B' and (resid 1 through 75 or (resid 76...BB1 - 101 - 10
24ASPASPLYSLYS(chain 'B' and (resid 1 through 75 or (resid 76...BB38 - 39738 - 397

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Components

#1: Protein carbon-sulfur lyase FnaPatB1


Mass: 47627.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-I3L / allyl-cysteine


Type: L-peptide linking / Mass: 161.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40 % PEG 300, 0.2 M magnesium chloride in 0.1 M sodium cacodylate-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.979511 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979511 Å / Relative weight: 1
ReflectionResolution: 2.6→47.43 Å / Num. obs: 36686 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 59.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.148 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4403 / CC1/2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QP2

6qp2


Resolution: 2.6→19.29 Å / SU ML: 0.3497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 1860 5.1 %
Rwork0.2145 34629 -
obs0.2173 36489 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6355 0 19 10 6384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876532
X-RAY DIFFRACTIONf_angle_d1.08538816
X-RAY DIFFRACTIONf_chiral_restr0.0579924
X-RAY DIFFRACTIONf_plane_restr0.00631125
X-RAY DIFFRACTIONf_dihedral_angle_d26.70392438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.33721420.2832605X-RAY DIFFRACTION99.93
2.67-2.750.31151490.25742602X-RAY DIFFRACTION100
2.75-2.840.29551420.26852623X-RAY DIFFRACTION99.96
2.84-2.940.35911470.25292606X-RAY DIFFRACTION100
2.94-3.060.31031450.24212638X-RAY DIFFRACTION99.93
3.06-3.190.31651390.23552642X-RAY DIFFRACTION100
3.19-3.360.29571140.23352650X-RAY DIFFRACTION100
3.36-3.570.2861320.22652661X-RAY DIFFRACTION99.96
3.57-3.840.29281560.20972634X-RAY DIFFRACTION99.96
3.84-4.230.2291390.19552690X-RAY DIFFRACTION100
4.23-4.830.24181390.18152702X-RAY DIFFRACTION100
4.83-6.050.23861480.21622724X-RAY DIFFRACTION100
6.06-19.290.24731680.20112852X-RAY DIFFRACTION99.77

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