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

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Basic information

Entry
Database: PDB / ID: 9flh
TitleCrystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing four 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 / SAD / Resolution: 1.5 Å
AuthorsAcebron, I. / Miguel-Ruano, V. / Straume, D. / Havarstein, L.S. / 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)14,6319
Polymers14,0741
Non-polymers5588
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-146 kcal/mol
Surface area5920 Å2
Unit cell
Length a, b, c (Å)56.861, 56.861, 32.334
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-405-

ZN

21AA-518-

HOH

31AA-522-

HOH

41AA-551-

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
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.: 5 / 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
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
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: 1.28 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2015
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.5→49.24 Å / Num. obs: 18745 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 25.74 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 0.998
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.335 / Mean I/σ(I) obs: 0.809 / Num. unique obs: 956 / Rsym value: 1.335 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXDEphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→32.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.651 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.242 963 5.137 %
Rwork0.196 --
obs-18745 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.545 Å20 Å2
2---1.09 Å20 Å2
3---3.537 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 14 67 926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.013911
X-RAY DIFFRACTIONr_bond_other_d0.0020.017773
X-RAY DIFFRACTIONr_angle_refined_deg2.7261.6661215
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5811799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.13522.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60615137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.19155
X-RAY DIFFRACTIONr_chiral_restr0.0710.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
X-RAY DIFFRACTIONr_nbd_refined0.2420.5179
X-RAY DIFFRACTIONr_nbd_other0.1880.524
X-RAY DIFFRACTIONr_nbtor_refined0.1790.5443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.550
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.51
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_refined0.2410.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5483.163432
X-RAY DIFFRACTIONr_mcbond_other2.5523.154428
X-RAY DIFFRACTIONr_mcangle_it4.0094.715535
X-RAY DIFFRACTIONr_mcangle_other4.0064.714535
X-RAY DIFFRACTIONr_scbond_it3.953.489478
X-RAY DIFFRACTIONr_scbond_other3.9463.494479
X-RAY DIFFRACTIONr_scangle_it5.255.118677
X-RAY DIFFRACTIONr_scangle_other5.2465.123678
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: 1.5→1.54 Å
RfactorNum. reflection% reflection
Rfree0.35 82 -
Rwork0.335 1329 -
obs--100 %

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