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- PDB-5u6f: Bacterial adhesin from Mobiluncus mulieris containing intramolecu... -

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Basic information

Entry
Database: PDB / ID: 5u6f
TitleBacterial adhesin from Mobiluncus mulieris containing intramolecular disulfide, isopeptide, and ester bond cross-links (space group P21)
ComponentsLPXTG-motif cell wall anchor domain protein
KeywordsCELL ADHESION / bacterial adhesin / Ig-like domain / intramolecular cross-link
Function / homologyDomain of unknown function DUF5979 / T-Q ester bond containing domain / T-Q ester bond containing domain / 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: 1.5 Å
AuthorsPaynter, J. / Young, P.G. / Squire, C.J.
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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.548, 51.604, 81.206
Angle α, β, γ (deg.)90.00, 101.60, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.15 %
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: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.5→79.547 Å / Num. obs: 43553 / % possible obs: 97.1 % / Redundancy: 7.4 % / CC1/2: 1 / Net I/σ(I): 22.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.7 / Num. measured obs: 2081 / CC1/2: 0.919 / % possible all: 95.5

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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 SAD model

Resolution: 1.5→79.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.193 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 2217 5.1 %RANDOM
Rwork0.23383 ---
obs0.23546 41295 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.294 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-0 Å2-1.26 Å2
2--2.96 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.5→79.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 0 124 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022183
X-RAY DIFFRACTIONr_bond_other_d0.0020.022053
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9622959
X-RAY DIFFRACTIONr_angle_other_deg0.81734757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99726.8686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.119153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
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_it0.8161.8681150
X-RAY DIFFRACTIONr_mcbond_other0.8141.8681149
X-RAY DIFFRACTIONr_mcangle_it1.3252.8011434
X-RAY DIFFRACTIONr_mcangle_other1.3242.81435
X-RAY DIFFRACTIONr_scbond_it1.1492.0061033
X-RAY DIFFRACTIONr_scbond_other1.1492.0061033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8472.9441525
X-RAY DIFFRACTIONr_long_range_B_refined2.8414.6712309
X-RAY DIFFRACTIONr_long_range_B_other2.80314.5872279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 193 -
Rwork0.31 2925 -
obs--95.24 %

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