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- PDB-6h2l: Receptor-binding domain of Proteus mirabilis Uroepithelial Cell A... -

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Basic information

Entry
Database: PDB / ID: 6h2l
TitleReceptor-binding domain of Proteus mirabilis Uroepithelial Cell Adhesin UcaD21-217
ComponentsPutative fimbrial adhesin
KeywordsCELL ADHESION / fimbriae / adhesin / Proteus mirabilis / urinary tract infection
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / Putative fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWangshu, J. / Knight, S.D.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.
Authors: Jiang, W. / Ubhayasekera, W. / Pearson, M.M. / Knight, S.D.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative fimbrial adhesin
B: Putative fimbrial adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,43811
Polymers43,5732
Non-polymers8659
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-103 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.473, 49.828, 61.833
Angle α, β, γ (deg.)86.45, 74.51, 75.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative fimbrial adhesin


Mass: 21786.621 Da / Num. of mol.: 2 / Mutation: Y25H
Source method: isolated from a genetically manipulated source
Details: The expression plasmid (pNIC-CH2) introduces an additional alanine between the target DNA insertion site and the C-terminal His-6 tag encoded by the plasmid.
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: PMI0533 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 pRARE2 / References: UniProt: B4EV65
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.91 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 2 M ammonium sulphate, 0.1 M bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→37.4 Å / Num. obs: 52581 / % possible obs: 96.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.97 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1181 / Rpim(I) all: 0.07172 / Rrim(I) all: 0.1387 / Net I/σ(I): 7.08
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.9651 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5178 / CC1/2: 0.53 / Rpim(I) all: 0.5974 / Rrim(I) all: 1.14 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H1X

6h1x


Resolution: 1.5→37.4 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2377 2570 4.89 %
Rwork0.2137 --
obs0.2149 52550 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 45 316 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073189
X-RAY DIFFRACTIONf_angle_d0.6974391
X-RAY DIFFRACTIONf_dihedral_angle_d8.0781880
X-RAY DIFFRACTIONf_chiral_restr0.052502
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52890.34931520.32632743X-RAY DIFFRACTION94
1.5289-1.56010.36141380.29942703X-RAY DIFFRACTION95
1.5601-1.5940.28791430.27752777X-RAY DIFFRACTION96
1.594-1.63110.32571280.27022714X-RAY DIFFRACTION96
1.6311-1.67190.30971360.26192794X-RAY DIFFRACTION96
1.6719-1.71710.27691430.24212758X-RAY DIFFRACTION96
1.7171-1.76760.24651470.22362766X-RAY DIFFRACTION96
1.7676-1.82460.23541750.2122711X-RAY DIFFRACTION96
1.8246-1.88980.21221610.19932770X-RAY DIFFRACTION97
1.8898-1.96550.2471140.21892781X-RAY DIFFRACTION96
1.9655-2.0550.22691440.19552820X-RAY DIFFRACTION97
2.055-2.16330.22321190.1932806X-RAY DIFFRACTION97
2.1633-2.29880.23741460.19962752X-RAY DIFFRACTION97
2.2988-2.47630.21631730.20252795X-RAY DIFFRACTION98
2.4763-2.72540.22431410.20222825X-RAY DIFFRACTION98
2.7254-3.11960.22211140.19912828X-RAY DIFFRACTION98
3.1196-3.92970.20841380.19352804X-RAY DIFFRACTION98
3.9297-37.6030.22721580.21092833X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.74990.13630.24340.9491-0.33750.4751-0.0104-0.124-0.01980.042-0.018-0.0038-0.12730.02160.0010.08660.003-0.00540.0818-0.00240.083353.249845.220265.1362
20.45770.17420.2591.2335-0.7791.0008-0.0021-0.02070.01090.0030.0490.0728-0.0505-0.03170.01180.0720.00350.00370.0574-0.00760.093147.943148.555756.5996
30.7330.1365-0.20020.81130.16240.5655-0.0288-0.0094-0.0354-0.13770.01880.0449-0.07960.1995-0.00720.1219-0.013-0.00720.0488-0.00920.082550.966541.413253.6622
40.76540.12750.13260.8526-0.13580.5287-0.01770.1501-0.0134-0.1212-0.0185-0.01670.03530.0584-0.02280.0565-0.0045-0.00660.0701-0.00330.065155.576223.945731.8166
50.552-0.0594-0.1980.3253-0.26590.66320.02470.01120.0067-0.0197-0.01890.00130.02510.02130.00020.0574-0.0093-0.00860.0650.00390.085246.292224.447436.533
60.62780.0438-0.17440.201-0.16850.29040.00170.08170.0433-0.06940.04020.05750.0435-0.02740.00240.0647-0.0013-0.01230.066-0.00660.078547.099223.166836.573
70.52350.04040.02580.56040.0280.13460.1976-0.06870.20650.0285-0.04590.1325-0.2760.04080.09080.10350.00840.01070.0636-0.01270.098144.972430.874447.8606
80.14870.0004-0.04470.0002-0.00420.01510.10320.2574-0.0447-0.02590.043-0.12020.2870.01340.0170.20830.03930.01390.2314-0.02340.167768.301922.593710.3604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 216 )
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 182 through 208 )
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 224 )

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