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- PDB-6h1x: Receptor-binding domain of Proteus mirabilis Uroepithelial Cell A... -

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Basic information

Entry
Database: PDB / ID: 6h1x
TitleReceptor-binding domain of Proteus mirabilis Uroepithelial Cell Adhesin UcaD21-211
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 / SAD / Resolution: 1.7 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 12, 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 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative fimbrial adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2463
Polymers21,1281
Non-polymers1182
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.350, 73.350, 153.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Putative fimbrial adhesin


Mass: 21127.893 Da / Num. of mol.: 1
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.005 M CoCl2, 1 M HEPES pH 7.5, 10-15% PEG 3350

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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 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: 1.7→41.89 Å / Num. obs: 23405 / % possible obs: 99.75 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1162 / Rpim(I) all: 0.04577 / Rrim(I) all: 0.1251 / Net I/σ(I): 10.18
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2269 / CC1/2: 0.699 / Rpim(I) all: 0.4643 / Rrim(I) all: 1.255 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→41.89 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2201 1232 5.27 %
Rwork0.1972 --
obs0.1984 23365 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 2 155 1623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041560
X-RAY DIFFRACTIONf_angle_d0.6752145
X-RAY DIFFRACTIONf_dihedral_angle_d8.408916
X-RAY DIFFRACTIONf_chiral_restr0.049244
X-RAY DIFFRACTIONf_plane_restr0.004284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.76770.30411280.3132373X-RAY DIFFRACTION98
1.7677-1.84820.32511390.25842422X-RAY DIFFRACTION100
1.8482-1.94560.24791400.24582411X-RAY DIFFRACTION100
1.9456-2.06750.23241570.21082408X-RAY DIFFRACTION100
2.0675-2.22710.2541280.19122437X-RAY DIFFRACTION100
2.2271-2.45120.25561200.20212464X-RAY DIFFRACTION100
2.4512-2.80590.18681590.19642465X-RAY DIFFRACTION100
2.8059-3.53480.19931250.18752515X-RAY DIFFRACTION100
3.5348-41.90540.20061360.17622639X-RAY DIFFRACTION100
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)
11.3828-0.0417-0.10351.4931-0.66990.30920.0773-0.220.00130.3005-0.1618-0.0286-0.24950.495300.2447-0.03360.00110.2683-0.00240.24313.5889-14.517-17.349
21.1433-0.56310.5770.43570.01450.96920.04820.13020.0247-0.05070.01040.04360.0320.07370.00010.2283-0.02340.0090.1830.00260.2443-5.0385-14.8767-30.5257
31.83740.9524-0.0681.1206-0.49481.23990.0293-0.3029-0.06310.1291-0.01970.0854-0.16220.0545-0.00010.30090.0066-0.0130.25360.02290.2445-3.6222-15.3489-15.607
40.3453-0.13220.21280.25980.05390.3669-0.0117-0.08520.0448-0.28050.05150.2344-0.1662-0.22150.00010.2719-0.01920.00440.20460.02240.293-7.9903-9.4445-25.3986
50.46440.1425-0.37540.5569-0.53641.3680.05080.00860.0290.0241-0.1016-0.0141-0.00270.1727-0.00010.2118-0.0172-0.01780.18270.00230.2248-2.8186-14.4216-24.0401
60.89230.5575-0.29191.30860.48130.82050.11810.0583-0.0932-0.0733-0.06660.02880.39470.26260.00030.24710.0157-0.00570.1795-0.00370.2274-3.9875-18.9393-36.3281
70.3096-0.14690.14650.3828-0.16830.09950.5325-0.3020.02440.60890.0338-0.28240.5129-0.33840.01180.4922-0.1128-0.07230.50560.03530.348611.6707-18.8354-3.9711
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 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 122 )
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 218 )

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