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- PDB-6i09: Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 6i09
TitleCrystal structure of RlpA SPOR domain from Pseudomonas aeruginosa in complex with denuded glycan obtained by soaking
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 / MOLECULAR REPLACEMENT / Resolution: 1.48 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: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolytic peptidoglycan transglycosylase RlpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2772
Polymers8,2881
Non-polymers9891
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint12 kcal/mol
Surface area4930 Å2
Unit cell
Length a, b, c (Å)67.433, 68.151, 38.994
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-525-

HOH

21A-573-

HOH

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Components

#1: Protein Endolytic peptidoglycan transglycosylase RlpA


Mass: 8288.415 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 988.937 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C]/1-2-3-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.72 %
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: 0.979257 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.48→47.934 Å / Num. obs: 15044 / % possible obs: 97.77 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.78 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Net I/σ(I): 14.8
Reflection shellResolution: 1.48→1.53 Å / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1475 / Rpim(I) all: 0.319

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I05

6i05


Resolution: 1.48→47.93 Å / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 748 4.98 %
Rwork0.1689 14277 -
obs0.1704 15025 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.48→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms576 0 68 73 717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052677
X-RAY DIFFRACTIONf_angle_d0.858929
X-RAY DIFFRACTIONf_chiral_restr0.0686120
X-RAY DIFFRACTIONf_plane_restr0.005118
X-RAY DIFFRACTIONf_dihedral_angle_d9.2297497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.590.26861410.22052854X-RAY DIFFRACTION99.17
1.59-1.750.23081520.1862861X-RAY DIFFRACTION99.47
1.75-2.010.20131550.15512835X-RAY DIFFRACTION98.13
2.01-2.530.19411390.17422879X-RAY DIFFRACTION98.24
2.53-47.930.18821610.16122848X-RAY DIFFRACTION94.09

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