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- PDB-9fln: Crystal structure of the C-terminal domain of VldE H373A from Str... -

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Basic information

Entry
Database: PDB / ID: 9fln
TitleCrystal structure of the C-terminal domain of VldE H373A from Streptococcus pneumoniae
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: 1.14 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)14,2034
Polymers14,0061
Non-polymers1963
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-66 kcal/mol
Surface area5940 Å2
Unit cell
Length a, b, c (Å)59.139, 59.139, 32.481
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-401-

ZN

21A-502-

HOH

31A-549-

HOH

41A-628-

HOH

51A-634-

HOH

61A-636-

HOH

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Components

#1: Protein LysM domain-containing protein


Mass: 14006.484 Da / Num. of mol.: 1 / Mutation: H373A
Source method: isolated from a genetically manipulated source
Details: THE N-TERMINAL G IS DERIVED FROM THE TAG USED TO PURIFY THE PROTEIN. HISTIDINE 373 IS MUTATED TO AN ALANINE.
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100 mM Hepes pH 7.2, 50 mM Cadmium sulfate and 0.6 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.2311
pseudo-merohedral22K, H, -L20.2737
pseudo-merohedral33-h,-k,l30.2128
pseudo-merohedral44-K, -H, -L40.2825
ReflectionResolution: 1.14→29.57 Å / Num. obs: 46365 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Net I/σ(I): 18.8
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.879 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2322 / CC1/2: 0.401 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→29.569 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.452 / SU ML: 0.011 / Cross valid method: FREE R-VALUE / ESU R: 0.005 / ESU R Free: 0.005
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1278 2404 5.185 %
Rwork0.1074 43958 -
all0.109 --
obs-46362 99.985 %
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: 18.184 Å2
Baniso -1Baniso -2Baniso -3
1--8.187 Å2-0 Å2-0 Å2
2---8.187 Å2-0 Å2
3---16.374 Å2
Refinement stepCycle: LAST / Resolution: 1.14→29.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 3 136 1028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.012950
X-RAY DIFFRACTIONr_bond_other_d0.0010.016846
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.7961293
X-RAY DIFFRACTIONr_angle_other_deg0.3581.7591957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.83856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65810148
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4061047
X-RAY DIFFRACTIONr_chiral_restr0.0480.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.1990.2199
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2859
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2477
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.250.219
X-RAY DIFFRACTIONr_nbd_other0.1610.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.229
X-RAY DIFFRACTIONr_mcbond_it1.7371.959474
X-RAY DIFFRACTIONr_mcbond_other1.7271.959473
X-RAY DIFFRACTIONr_mcangle_it2.6613.523597
X-RAY DIFFRACTIONr_mcangle_other2.6613.522598
X-RAY DIFFRACTIONr_scbond_it1.7292.059476
X-RAY DIFFRACTIONr_scbond_other1.7212.059476
X-RAY DIFFRACTIONr_scangle_it2.733.736694
X-RAY DIFFRACTIONr_scangle_other2.7283.735695
X-RAY DIFFRACTIONr_lrange_it7.57923.5951160
X-RAY DIFFRACTIONr_lrange_other6.35222.4711118
X-RAY DIFFRACTIONr_rigid_bond_restr1.07531796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.3642100.3363198X-RAY DIFFRACTION99.8243
1.17-1.2020.3051640.2563214X-RAY DIFFRACTION100
1.202-1.2360.2191530.1873082X-RAY DIFFRACTION100
1.236-1.2740.1781500.1352986X-RAY DIFFRACTION100
1.274-1.3160.1331000.1192941X-RAY DIFFRACTION99.9671
1.316-1.3620.1611940.1042743X-RAY DIFFRACTION100
1.362-1.4130.1111520.0952751X-RAY DIFFRACTION100
1.413-1.4710.1241400.0862594X-RAY DIFFRACTION100
1.471-1.5360.1131300.0932523X-RAY DIFFRACTION100
1.536-1.6110.1211520.0982340X-RAY DIFFRACTION100
1.611-1.6980.1211300.1022273X-RAY DIFFRACTION100
1.698-1.80.1261300.1142140X-RAY DIFFRACTION100
1.8-1.9240.1361280.1162021X-RAY DIFFRACTION100
1.924-2.0780.1491080.1071842X-RAY DIFFRACTION100
2.078-2.2750.129760.1081763X-RAY DIFFRACTION100
2.275-2.5420.129830.111548X-RAY DIFFRACTION100
2.542-2.9310.142580.1151427X-RAY DIFFRACTION100
2.931-3.5810.146570.091162X-RAY DIFFRACTION100
3.581-5.0280.072620.08886X-RAY DIFFRACTION100
5.028-29.5690.131270.122524X-RAY DIFFRACTION100

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