+Open data
-Basic information
Entry | Database: PDB / ID: 2q7a | ||||||
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Title | Crystal structure of the cell surface heme transfer protein Shp | ||||||
Components | Cell surface heme-binding protein | ||||||
Keywords | heme binding protein / beta sandwich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Aranda IV, R. / Worley, C.E. / Bitto, E. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp. Authors: Aranda IV, R. / Worley, C.E. / Liu, M. / Bitto, E. / Cates, M.S. / Olson, J.S. / Lei, B. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q7a.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q7a.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 2q7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q7a ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q7a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | there are two biological units of Shp180 in the asymmetric unit. |
-Components
#1: Protein | Mass: 16619.590 Da / Num. of mol.: 2 / Fragment: Shp180 / Mutation: C37S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: shp / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06A48 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #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: 3.12 Å3/Da / Density % sol: 60.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.8M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→80 Å / Num. obs: 23738 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.115 / Χ2: 1.035 / Net I/σ(I): 20.4 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1496 / Χ2: 0.934 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→41.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.359 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.782 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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