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Yorodumi- PDB-6y4f: X-ray structure of the Zn-dependent receptor-binding domain of Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y4f | ||||||
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Title | X-ray structure of the Zn-dependent receptor-binding domain of Proteus mirabilis MR/P fimbrial adhesin MrpH | ||||||
Components | Fimbrial adhesin | ||||||
Keywords | CELL ADHESION / Metal binding protein / adhesin | ||||||
Function / homology | Fimbrial-type adhesion domain superfamily / pilus / cell adhesion / GLUTAMIC ACID / Fimbrial adhesin Function and homology information | ||||||
Biological species | Proteus mirabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Knight, S.D. / Ubhayasekera, W. / Jiang, W. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Plos Pathog. / Year: 2020 Title: MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation. Authors: Jiang, W. / Ubhayasekera, W. / Breed, M.C. / Norsworthy, A.N. / Serr, N. / Mobley, H.L.T. / Pearson, M.M. / Knight, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y4f.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4f.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4f ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4f | HTTPS FTP |
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-Related structure data
Related structure data | 6y4eSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15550.442 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria) Gene: mrpH, PMI0270 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B4EUK6 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GLU / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus HT screen (Molecular Dimensions, UK) condition D9 (0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, ...Details: Morpheus HT screen (Molecular Dimensions, UK) condition D9 (0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M bicine/Trizma base pH 8.5, 10% w/v PEG 20000 and 20% v/v PEG MME 550) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.05 Å / Num. obs: 12317 / % possible obs: 98.97 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.18 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.75→1.813 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 7707 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.242 / Rrim(I) all: 0.614 / % possible all: 93.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y4E Resolution: 1.75→19.05 Å / SU ML: 0.1464 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.0833
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.05 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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