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Yorodumi- PDB-8ehe: Structure of Tannerella forsythia potempin C in complex with mirolase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ehe | ||||||
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Title | Structure of Tannerella forsythia potempin C in complex with mirolase | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR / Serine-peptidase inhibitor / HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Tannerella forsythia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Gomis-Ruth, F.X. | ||||||
Funding support | 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia. Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. ...Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. / Enghild, J.J. / Cuppari, A. / Arolas, J.L. / de Diego, I. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T. / Dive, V. / Zani, M.L. / Moreau, T. / Potempa, J. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ehe.cif.gz | 379.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ehe.ent.gz | 307.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ehe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ehe_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 8ehe_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 8ehe_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 8ehe_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/8ehe ftp://data.pdbj.org/pub/pdb/validation_reports/eh/8ehe | HTTPS FTP |
-Related structure data
Related structure data | 8b2mC 8b2nC 8b2qC 8ehbC 8ehcC 8ehdC 1st3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37594.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7KVG3 |
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#2: Protein | Mass: 16974.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: CLI86_13365, TFUB20_02175 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UUC0 |
-Non-polymers , 5 types, 769 molecules
#3: Chemical | ChemComp-NA / | ||||||
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#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The PotC:mirolase complex at 10 mg/mL in 2 mM calcium chloride, 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 19 % (w/v) PEG 2,000 MME in 100 mM of a mixture of succinic ...Details: The PotC:mirolase complex at 10 mg/mL in 2 mM calcium chloride, 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 19 % (w/v) PEG 2,000 MME in 100 mM of a mixture of succinic acid, sodium dihydrogen phosphate, and glycine at molar ratios 2:7:7, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→56.7 Å / Num. obs: 184353 / % possible obs: 96.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.1→1.17 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 26672 / CC1/2: 0.79 / Rrim(I) all: 0.74 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ST3 Resolution: 1.1→42.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.978 / SU R Cruickshank DPI: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.028 / SU Rfree Blow DPI: 0.028 / SU Rfree Cruickshank DPI: 0.026
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Displacement parameters | Biso mean: 14.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.1→42.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.13 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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