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- PDB-5u5o: Bacterial adhesin from Mobiluncus mulieris containing intramolecu... -

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Basic information

Entry
Database: PDB / ID: 5u5o
TitleBacterial adhesin from Mobiluncus mulieris containing intramolecular disulfide, isopeptide, and ester bond cross-links (space group P1)
ComponentsLPXTG-motif cell wall anchor domain protein
KeywordsCELL ADHESION / bacterial adhesin / Ig-like domain / intramolecular cross-link
Function / homologyT-Q ester bond containing domain / T-Q ester bond containing domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / membrane / LPXTG-motif cell wall anchor domain protein
Function and homology information
Biological speciesMobiluncus mulieris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsPaynter, J. / Young, P.G. / Squire, C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of NZ Marsden Fund New Zealand
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium.
Authors: Young, P.G. / Paynter, J.M. / Wardega, J.K. / Middleditch, M.J. / Payne, L.S. / Baker, E.N. / Squire, C.J.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _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: LPXTG-motif cell wall anchor domain protein


Theoretical massNumber of molelcules
Total (without water)31,3891
Polymers31,3891
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.900, 54.983, 57.317
Angle α, β, γ (deg.)67.72, 76.47, 85.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LPXTG-motif cell wall anchor domain protein


Mass: 31388.865 Da / Num. of mol.: 1 / Fragment: UNP residues 6668-6959
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mobiluncus mulieris (bacteria) / Plasmid: pPROEX-Hta / Production host: Escherichia coli (E. coli) / References: UniProt: E0QN07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (v/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate), and 0.1 M MES/Imidazole (pH 6.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.15→19.15 Å / Num. obs: 102468 / % possible obs: 94.1 % / Redundancy: 7.9 % / CC1/2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1 / Num. measured obs: 4921 / CC1/2: 0.549 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 1.15→19.15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.376 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21054 5177 5.1 %RANDOM
Rwork0.18141 ---
obs0.18289 97278 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0.03 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.15→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 326 2486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022276
X-RAY DIFFRACTIONr_bond_other_d0.0020.022150
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9613101
X-RAY DIFFRACTIONr_angle_other_deg0.84234999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485.033307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62526.96689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5115398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.08153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
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_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8581.6621194
X-RAY DIFFRACTIONr_mcbond_other1.8581.6611193
X-RAY DIFFRACTIONr_mcangle_it2.472.5061504
X-RAY DIFFRACTIONr_mcangle_other2.4692.5071505
X-RAY DIFFRACTIONr_scbond_it2.0691.8861082
X-RAY DIFFRACTIONr_scbond_other2.0681.8861082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5752.7241595
X-RAY DIFFRACTIONr_long_range_B_refined3.63115.3322658
X-RAY DIFFRACTIONr_long_range_B_other3.39614.3042487
X-RAY DIFFRACTIONr_rigid_bond_restr1.92834426
X-RAY DIFFRACTIONr_sphericity_free28.253562
X-RAY DIFFRACTIONr_sphericity_bonded15.49154647
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 375 -
Rwork0.281 6942 -
obs--90.57 %

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