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

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Basic information

Entry
Database: PDB / ID: 9flm
TitleCrystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae in a catalytically competent conformation
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: 1.5 Å
AuthorsMiguel-Ruano, V. / Acebron, I. / P.de Jose, U. / 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
A: LysM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3355
Polymers14,0741
Non-polymers2624
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PISA Software determined quaternary structure: Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-103 kcal/mol
Surface area5970 Å2
Unit cell
Length a, b, c (Å)57.111, 57.111, 32.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-402-

ZN

21A-571-

HOH

31A-590-

HOH

41A-629-

HOH

51A-633-

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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 43.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Hepes pH 7.5, 50 mM Cadmium sulfate and 1 M of Sodium acetate, soaked with 20 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5171
pseudo-merohedral22-h,-k,l20.4829
ReflectionResolution: 1.5→28.56 Å / Num. obs: 18946 / % possible obs: 99.3 % / Redundancy: 10.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.109 / Net I/σ(I): 6.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.759 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 921 / CC1/2: 0.715 / Rpim(I) all: 0.864 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.556 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.448 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.016
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1987 912 4.818 %
Rwork0.1655 18016 -
all0.167 --
obs-18928 99.131 %
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: 29.239 Å2
Baniso -1Baniso -2Baniso -3
1--15.593 Å2-0 Å2-0 Å2
2---15.593 Å2-0 Å2
3---31.187 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 4 133 1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.012947
X-RAY DIFFRACTIONr_bond_other_d0.0010.016838
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.7971288
X-RAY DIFFRACTIONr_angle_other_deg0.3791.7621938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.96556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98710146
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8221048
X-RAY DIFFRACTIONr_chiral_restr0.050.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.1870.2242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.2858
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2475
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.219
X-RAY DIFFRACTIONr_nbd_other0.1330.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2940.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.270.21
X-RAY DIFFRACTIONr_mcbond_it1.2982.825469
X-RAY DIFFRACTIONr_mcbond_other1.2922.826468
X-RAY DIFFRACTIONr_mcangle_it2.1755.076589
X-RAY DIFFRACTIONr_mcangle_other2.1735.073590
X-RAY DIFFRACTIONr_scbond_it1.0442.896478
X-RAY DIFFRACTIONr_scbond_other1.0422.895478
X-RAY DIFFRACTIONr_scangle_it1.7555.285697
X-RAY DIFFRACTIONr_scangle_other1.7545.282698
X-RAY DIFFRACTIONr_lrange_it5.50233.3171205
X-RAY DIFFRACTIONr_lrange_other5.17331.6781160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3231050.2671270X-RAY DIFFRACTION97.7257
1.539-1.5810.237580.1971281X-RAY DIFFRACTION97.8801
1.581-1.6270.204640.1731262X-RAY DIFFRACTION98.5141
1.627-1.6770.204420.1531231X-RAY DIFFRACTION99.1433
1.677-1.7310.224480.1791210X-RAY DIFFRACTION98.2045
1.731-1.7920.227830.1731101X-RAY DIFFRACTION100
1.792-1.8590.177680.1771115X-RAY DIFFRACTION98.7479
1.859-1.9350.256400.2121095X-RAY DIFFRACTION98.6099
1.935-2.020.22440.1691011X-RAY DIFFRACTION100
2.02-2.1190.183320.1791017X-RAY DIFFRACTION99.0557
2.119-2.2320.159520.162889X-RAY DIFFRACTION99.5767
2.232-2.3670.268480.175904X-RAY DIFFRACTION99.6859
2.367-2.5290.168520.173826X-RAY DIFFRACTION99.8862
2.529-2.730.212420.193782X-RAY DIFFRACTION99.8788
2.73-2.9880.21320.189721X-RAY DIFFRACTION99.8674
2.988-3.3360.251200.171644X-RAY DIFFRACTION100
3.336-3.8430.194340.139572X-RAY DIFFRACTION100
3.843-4.6860.146240.135489X-RAY DIFFRACTION100
4.686-6.540.169180.139377X-RAY DIFFRACTION100
6.54-28.5560.13360.157219X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.218 Å / Origin y: -0.1301 Å / Origin z: -8.3963 Å
111213212223313233
T0.0505 Å2-0.0012 Å20.0019 Å2-0.0611 Å20.0077 Å2--0.0125 Å2
L0.8294 °20.0228 °20.0535 °2-0.4013 °20.0783 °2--0.1363 °2
S-0.0326 Å °-0.0131 Å °-0.0301 Å °-0.0388 Å °0.016 Å °-0.0446 Å °-0.0334 Å °0.0139 Å °0.0166 Å °
Refinement TLS groupSelection: ALL

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