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- PDB-9flk: Crystal structure of the C-terminal domain of VldE from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 9flk
TitleCrystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing two zinc atoms at the binding site
ComponentsLysM domain-containing protein
KeywordsMETAL BINDING PROTEIN / PEPTIDOGLYCAN HYDROLASE / PNEUMOCOCCAL CELL-WALL METABOLISM / ZINC-BINDING PROTEIN / LYSM-CONTAINING PROTEIN
Function / homologyLysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / : / LysM domain-containing protein
Function and homology information
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAcebron, I. / Miguel-Ruano, V. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPRE2018-085033 Spain
CitationJournal: Acs Catalysis / Year: 2024
Title: Characterization of VldE (Spr1875), a Pneumococcal Two-State l,d-Endopeptidase with a Four-Zinc Cluster in the Active Site.
Authors: Miguel-Ruano, V. / Acebron, I. / Lee, M. / Martin-Galiano, A.J. / Freton, C. / de Jose, U.P. / Ramachandran, B. / Gago, F. / Kjos, M. / Hesek, D. / Grangeasse, C. / Havarstein, L.S. / ...Authors: Miguel-Ruano, V. / Acebron, I. / Lee, M. / Martin-Galiano, A.J. / Freton, C. / de Jose, U.P. / Ramachandran, B. / Gago, F. / Kjos, M. / Hesek, D. / Grangeasse, C. / Havarstein, L.S. / Straume, D. / Mobashery, S. / Hermoso, J.A.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: LysM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3825
Polymers14,0741
Non-polymers3094
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-101 kcal/mol
Surface area6280 Å2
Unit cell
Length a, b, c (Å)59.121, 59.121, 32.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11AA-403-

ZN

21AA-502-

HOH

31AA-586-

HOH

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Components

#1: Protein LysM domain-containing protein


Mass: 14073.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE N-TERMINAL G IS DERIVED FROM THE TAG USED TO PURIFY THE PROTEIN ARG314 SIDE CHAIN IS NOT IN THE PDB FILE DUE TO THE LACK OF ELECTRON DENSITY
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: spr1875 / Plasmid: PRSET-CHIC-TEV / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8DN78
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM TRIS-HCL, pH 8.5, 50 mM CADMIUM SULFATE, 1 M SODIUM ACETATE
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2019
RadiationMonochromator: CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.85→32.68 Å / Num. obs: 10367 / % possible obs: 94.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 8.9
Reflection shellResolution: 1.85→1.85 Å / Redundancy: 10 % / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 684 / Rsym value: 1.308 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPR1875 C-TERMINAL DOMAIN

Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.168 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.258 470 4.543 %
Rwork0.213 --
obs-10346 94.6 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.155 Å20 Å2
2--0.31 Å20 Å2
3----1.005 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 4 100 966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.013900
X-RAY DIFFRACTIONr_bond_other_d0.0020.017756
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6531209
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5781765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25723.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96815133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.184153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021023
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02190
X-RAY DIFFRACTIONr_nbd_refined0.1840.15189
X-RAY DIFFRACTIONr_nbd_other0.1150.1516
X-RAY DIFFRACTIONr_nbtor_refined0.160.15439
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.1564
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.11
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_refined0.0380.11
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1513.5438
X-RAY DIFFRACTIONr_mcbond_other3.1413.498436
X-RAY DIFFRACTIONr_mcangle_it4.7065.21544
X-RAY DIFFRACTIONr_mcangle_other4.7035.209544
X-RAY DIFFRACTIONr_scbond_it4.3243.83462
X-RAY DIFFRACTIONr_scbond_other4.2523.829460
X-RAY DIFFRACTIONr_scangle_it5.7995.632664
X-RAY DIFFRACTIONr_scangle_other5.7985.632665
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.52 36 -
Rwork0.502 763 -
obs--100 %

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