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Yorodumi- PDB-3vtm: Structure of heme transport protein IsdH-NEAT3 from S. aureus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vtm | ||||||
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Title | Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin | ||||||
Components | Iron-regulated surface determinant protein H | ||||||
Keywords | HEME-BINDING PROTEIN / Indium / metalloporphyrin / metal selectivity / NEAT domain / Heme binding / Heme transport / Hemin / PPIX / cell wall | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Vu, N.T. / Caaveiro, J.M.M. / Moriwaki, Y. / Tsumoto, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus Authors: Vu, N.T. / Moriwaki, Y. / Caaveiro, J.M.M. / Terada, T. / Tsutsumi, H. / Hamachi, I. / Shimizu, K. / Tsumoto, K. #1: Journal: Biochemistry / Year: 2011 Title: Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus. Authors: Moriwaki, Y. / Caaveiro, J.M. / Tanaka, Y. / Tsutsumi, H. / Hamachi, I. / Tsumoto, K. #2: Journal: J.Biol.Chem. / Year: 2008 Title: Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus. Authors: Watanabe, M. / Tanaka, Y. / Suenaga, A. / Kuroda, M. / Yao, M. / Watanabe, N. / Arisaka, F. / Ohta, T. / Tanaka, I. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vtm.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vtm.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/3vtm ftp://data.pdbj.org/pub/pdb/validation_reports/vt/3vtm | HTTPS FTP |
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-Related structure data
Related structure data | 3qugS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13003.636 Da / Num. of mol.: 2 / Fragment: NEAT domain, UNP RESIDUES 543-655 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: strain Mu50 / ATCC 700699 / Gene: harA, isdH, IsdH-NEAT3, sasI, SAV1731 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q931P4 #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 51.94 % / Mosaicity: 1.02 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG-MME 3500, Sodium Iodide 0.2M, Potassium iodide 0.2M, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→51.822 Å / Num. all: 6932 / Num. obs: 6932 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.146 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QUG Resolution: 2.8→51.82 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2688 / WRfactor Rwork: 0.2039 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7031 / SU B: 20.159 / SU ML: 0.403 / SU Rfree: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.73 Å2 / Biso mean: 31.5934 Å2 / Biso min: 9.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→51.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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