+Open data
-Basic information
Entry | Database: PDB / ID: 8glo | ||||||
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Title | Haemophilus parainfluenzae Holo HphA | ||||||
Components | Hemophilin | ||||||
Keywords | METAL TRANSPORT / Heme Binding / Hemophore / Type XI Secretion System Cargo / Beta Barrel | ||||||
Function / homology | HEME B/C Function and homology information | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å | ||||||
Authors | Shin, H.E. / Ng, D. / Moraes, T.F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Bacteriol. / Year: 2024 Title: Prevalence of Slam-dependent hemophilins in Gram-negative bacteria. Authors: Shin, H.E. / Pan, C. / Curran, D.M. / Bateman, T.J. / Chong, D.H.Y. / Ng, D. / Shah, M. / Moraes, T.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8glo.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8glo.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 8glo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/8glo ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8glo | HTTPS FTP |
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-Related structure data
Related structure data | 8gm3C 8gmmC 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
#1: Protein | Mass: 27471.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-HEB / |
#3: Chemical | ChemComp-CL / |
#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: 2.85 Å3/Da / Density % sol: 56.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Microseeding using seed stock obtained from 2.4 M sodium malonate pH 7.0 into final hit condition: 0.1M Tris-HCl pH 8.52 and 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979328 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979328 Å / Relative weight: 1 |
Reflection | Resolution: 1.937→39.3 Å / Num. obs: 24073 / % possible obs: 99.81 % / Redundancy: 11.3 % / CC1/2: 0.998 / Net I/σ(I): 12.23 |
Reflection shell | Resolution: 1.937→2.006 Å / Num. unique obs: 2366 / CC1/2: 0.892 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.937→39.3 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.937→39.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 36.4487 Å / Origin y: 24.9067 Å / Origin z: 44.4421 Å
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Refinement TLS group | Selection details: all |