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

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Basic information

Entry
Database: PDB / ID: 9flj
TitleCrystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing three 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 / ACETATE ION / : / LysM domain-containing protein
Function and homology information
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)14,5077
Polymers14,0741
Non-polymers4336
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-108 kcal/mol
Surface area6070 Å2
Unit cell
Length a, b, c (Å)57.192, 57.192, 32.506
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-541-

HOH

21AA-553-

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
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 MM HEPES, PH 7.5, 50 MM CADMIUM SULFATE, 1 M SODIUM ACETATE, 5 MM EDTA
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.2837 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.7157
11-h,-k,l20.2843
ReflectionResolution: 1.6→28.6 Å / Num. obs: 15644 / % possible obs: 99.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 7.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 753 / CC1/2: 0.381 / % 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: C-TERMINAL DOMAIN OF SPR1875 CONTAINING FOUR ZINC ATOMS

Resolution: 1.6→28.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.958 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.254 741 4.737 %
Rwork0.218 --
obs-15643 99.7 %
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: 30.17 Å2
Baniso -1Baniso -2Baniso -3
1--12.39 Å20 Å20 Å2
2---12.39 Å20 Å2
3---24.779 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 9 76 936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013910
X-RAY DIFFRACTIONr_bond_other_d0.0010.017770
X-RAY DIFFRACTIONr_angle_refined_deg1.761.661211
X-RAY DIFFRACTIONr_angle_other_deg1.21.581792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28922.54951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.001155
X-RAY DIFFRACTIONr_chiral_restr0.0620.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined0.1870.2200
X-RAY DIFFRACTIONr_nbd_other0.1330.221
X-RAY DIFFRACTIONr_nbtor_refined0.170.2431
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
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_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1943.109433
X-RAY DIFFRACTIONr_mcbond_other2.1873.104430
X-RAY DIFFRACTIONr_mcangle_it3.2884.653537
X-RAY DIFFRACTIONr_mcangle_other3.2864.652537
X-RAY DIFFRACTIONr_scbond_it2.7483.345475
X-RAY DIFFRACTIONr_scbond_other2.6743.342472
X-RAY DIFFRACTIONr_scangle_it3.4594.92672
X-RAY DIFFRACTIONr_scangle_other3.4564.922673
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: 1.6→1.64 Å
RfactorNum. reflection% reflection
Rfree0.372 90 -
Rwork0.262 1054 -
obs--99.91 %

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