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Yorodumi- PDB-7uc3: Intramolecular ester bond-containing repeat domain from G. berger... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uc3 | ||||||
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Title | Intramolecular ester bond-containing repeat domain from G. bergeri adhesin | ||||||
Components | Adhesin | ||||||
Keywords | CELL ADHESION / Repeat domain / adhesin / intramolecular ester bond / Ig-like fold | ||||||
Function / homology | T-Q ester bond containing domain / T-Q ester bond containing domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / membrane / Putative Cna protein B-type domain protein Function and homology information | ||||||
Biological species | Gemella bergeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.442 Å | ||||||
Authors | Wardega, J.K. / Squire, C.J. / Young, P.G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Intramolecular ester bond-containing repeat domain from G. bergeri adhesin Authors: Wardega, J.K. / Squire, C.J. / Young, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uc3.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uc3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7uc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/7uc3 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/7uc3 | HTTPS FTP |
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-Related structure data
Related structure data | 4ni6S S: Starting model for refinement |
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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
#1: Protein | Mass: 17036.812 Da / Num. of mol.: 1 / Fragment: Repeat domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gemella bergeri (bacteria) / Gene: HMPREF1983_01328 / Plasmid: pProEXHta / Production host: Escherichia coli (E. coli) / References: UniProt: U2Q1B9 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.31 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris Cl, and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.442→48.533 Å / Num. obs: 24975 / % possible obs: 96.8 % / Redundancy: 26.5 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.013 / Rrim(I) all: 0.068 / Χ2: 0.52 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 16.7 % / Num. unique obs: 713 / CC1/2: 0.479 / Rpim(I) all: 0.354 / % possible all: 58.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ni6 Resolution: 1.442→48.533 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.055 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.076 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.442→48.533 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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