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- PDB-6y4f: X-ray structure of the Zn-dependent receptor-binding domain of Pr... -
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Open data
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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 | ||||||
![]() | Fimbrial adhesin | ||||||
![]() | CELL ADHESION / Metal binding protein / adhesin | ||||||
Function / homology | Fimbrial-type adhesion domain superfamily / pilus / cell adhesion / GLUTAMIC ACID / Fimbrial adhesin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Knight, S.D. / Ubhayasekera, W. / Jiang, W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.9 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y4eSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: mrpH, PMI0270 / Production host: ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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