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Yorodumi- PDB-2r7a: Crystal Structure of a Periplasmic Heme Binding Protein from Shig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r7a | ||||||
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Title | Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae | ||||||
Components | Bacterial heme binding protein | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein / heme transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella dysenteriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ho, W.W. / Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins. Authors: Ho, W.W. / Li, H. / Eakanunkul, S. / Tong, Y. / Wilks, A. / Guo, M. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r7a.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r7a.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 2r7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r7a_validation.pdf.gz | 865.5 KB | Display | wwPDB validaton report |
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Full document | 2r7a_full_validation.pdf.gz | 892.7 KB | Display | |
Data in XML | 2r7a_validation.xml.gz | 45 KB | Display | |
Data in CIF | 2r7a_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/2r7a ftp://data.pdbj.org/pub/pdb/validation_reports/r7/2r7a | HTTPS FTP |
-Related structure data
Related structure data | 2r79SC 2rg7C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27582.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Strain: pSHU262 / Plasmid: pSHU262 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O70018 #2: Chemical | ChemComp-HEM / | #3: 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: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1M sodium citrate, 0.05M ammonium bromide, 15% polyethylene glycol 4000, 0.001M hemin chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→43.86 Å / Num. obs: 63384 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.01 / Rsym value: 0.67 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model of PhuT, PDB ENTRY 2R79 Resolution: 2.05→43.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1452602.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0413 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→43.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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