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- PDB-6i05: Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6i05
TitleCrystal structure of RlpA SPOR domain from Pseudomonas aeruginosa
ComponentsEndolytic peptidoglycan transglycosylase RlpA
KeywordsCELL CYCLE / Lytic transglycosylase / septum / SPOR domain / cell division / divisome / murein / denuded glycan
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic endotransglycosylase activity / peptidoglycan metabolic process / peptidoglycan binding / cell outer membrane / cell wall organization / plasma membrane
Similarity search - Function
Rare lipoprotein A / Endolytic peptidoglycan transglycosylase RlpA / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / RlpA-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Endolytic peptidoglycan transglycosylase RlpA / Endolytic peptidoglycan transglycosylase RlpA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.213 Å
AuthorsAlcorlo, M. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-59389-P and BFU2017-90030-P to JAH Spain
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of denuded glycan recognition by SPOR domains in bacterial cell division.
Authors: Alcorlo, M. / Dik, D.A. / De Benedetti, S. / Mahasenan, K.V. / Lee, M. / Dominguez-Gil, T. / Hesek, D. / Lastochkin, E. / Lopez, D. / Boggess, B. / Mobashery, S. / Hermoso, J.A.
History
DepositionOct 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolytic peptidoglycan transglycosylase RlpA


Theoretical massNumber of molelcules
Total (without water)8,3591
Polymers8,3591
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.588, 68.765, 38.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-538-

HOH

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Components

#1: Protein Endolytic peptidoglycan transglycosylase RlpA


Mass: 8359.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rlpA, PAMH19_1027 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A8RDC6, UniProt: Q9X6V6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M NaF and 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.21→34.383 Å / Num. obs: 24714 / % possible obs: 89.11 % / Redundancy: 3 % / Biso Wilson estimate: 12.93 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Net I/σ(I): 16.46
Reflection shellResolution: 1.21→1.257 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 911

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.213→34.38 Å / SU ML: 0.0902 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.8247
RfactorNum. reflection% reflection
Rfree0.1712 3557 8.17 %
Rwork0.1529 --
obs0.1545 24712 82.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.68 Å2
Refinement stepCycle: LAST / Resolution: 1.213→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 141 708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046599
X-RAY DIFFRACTIONf_angle_d0.7812823
X-RAY DIFFRACTIONf_chiral_restr0.0714101
X-RAY DIFFRACTIONf_plane_restr0.0041109
X-RAY DIFFRACTIONf_dihedral_angle_d8.4456483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.213-1.230.2575140.2198190X-RAY DIFFRACTION10
1.23-1.250.2439450.2004488X-RAY DIFFRACTION24.73
1.25-1.270.2222700.1887739X-RAY DIFFRACTION38.32
1.27-1.290.2513900.18271099X-RAY DIFFRACTION56.32
1.29-1.310.20861300.17361312X-RAY DIFFRACTION68.73
1.31-1.330.1911230.15751501X-RAY DIFFRACTION76.24
1.33-1.350.1841360.14841664X-RAY DIFFRACTION85.55
1.35-1.380.16151540.1491777X-RAY DIFFRACTION89.98
1.38-1.410.16961550.14821809X-RAY DIFFRACTION92.16
1.41-1.440.17151690.14331793X-RAY DIFFRACTION92.46
1.44-1.470.16711670.14471784X-RAY DIFFRACTION93.71
1.47-1.510.16251680.14351859X-RAY DIFFRACTION94.76
1.51-1.550.14811760.1341848X-RAY DIFFRACTION94.49
1.55-1.590.19291580.13111769X-RAY DIFFRACTION92.38
1.59-1.650.17751510.1431861X-RAY DIFFRACTION95.31
1.65-1.70.18151580.1431868X-RAY DIFFRACTION96.52
1.7-1.770.20261680.15091903X-RAY DIFFRACTION96.64
1.77-1.850.17511660.1521871X-RAY DIFFRACTION96.27
1.85-1.950.18011590.14311836X-RAY DIFFRACTION94.46
1.95-2.070.18261610.14591843X-RAY DIFFRACTION94.39
2.07-2.230.15381610.14791778X-RAY DIFFRACTION91.98
2.23-2.460.16031740.1521870X-RAY DIFFRACTION96.51
2.46-2.810.16271650.16831900X-RAY DIFFRACTION96.59
2.81-3.540.16321720.15761816X-RAY DIFFRACTION94.58
3.54-34.380.17261670.15771779X-RAY DIFFRACTION91.32

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