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Yorodumi- PDB-6ewm: Crystal structure of heme free PORPHYROMONAS GINGIVALIS HEME-BIND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ewm | |||||||||
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Title | Crystal structure of heme free PORPHYROMONAS GINGIVALIS HEME-BINDING PROTEIN HMUY | |||||||||
Components | Haemophore HmuY | |||||||||
Keywords | CELL INVASION / heme-binding protein | |||||||||
Function / homology | HmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / HmuY Function and homology information | |||||||||
Biological species | Porphyromonas gingivalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Antonyuk, S.V. / Strange, R.W. / Bielecki, M. / Olczak, T. / Olczak, M. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Biosci. Rep. / Year: 2018 Title: Tannerella forsythiaTfo belongs toPorphyromonas gingivalisHmuY-like family of proteins but differs in heme-binding properties. Authors: Bielecki, M. / Antonyuk, S. / Strange, R.W. / Smalley, J.W. / Mackiewicz, P. / Smiga, M. / Stepien, P. / Olczak, M. / Olczak, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ewm.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ewm.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ewm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ewm_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 6ewm_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 6ewm_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6ewm_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/6ewm ftp://data.pdbj.org/pub/pdb/validation_reports/ew/6ewm | HTTPS FTP |
-Related structure data
Related structure data | 6eu8C 3h8tS 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: 21227.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) Gene: hmuY', hmuY, AT291_03715, PGIN_13-1_01941, PGIN_YH522_00859 Plasmid: pHmuY11 / Production host: Escherichia coli (E. coli) / References: UniProt: A2I2W2 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.4 M ammonium sulphate, 100 mM MES pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2017 |
Radiation | Monochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→90.9 Å / Num. obs: 86584 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.014 / Rpim(I) all: 0.01 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3231 / CC1/2: 0.68 / Rpim(I) all: 0.43 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3h8t Resolution: 1.4→90.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.874 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.467 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→90.49 Å
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Refine LS restraints |
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