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Yorodumi- PDB-4h59: Crystal structure of iron uptake ABC transporter substrate-bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h59 | ||||||
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Title | Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to Bis-tris propane | ||||||
Components | Iron-compound ABC transporter, iron compound-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA AND BETA PROTEIN / PERIPLASMIC BINDING PROTEIN TYPE III FOLD / iron transport / iron uptake ABC transport system substrate binding protein / HYDROXYMATE SIDEROPHORE / putative membrane-anchored lipoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.658 Å | ||||||
Authors | Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to Bis-tris propane Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h59.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h59.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 4h59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h59_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4h59_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4h59_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4h59_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/4h59 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h59 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33967.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: SpneCM_010100006939 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97R09, UniProt: Q8DPY6*PLUS | ||
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#2: Chemical | ChemComp-B3P / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 M ammonium citrate pH 7.0, 0.1 M Bis-tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→30 Å / Num. obs: 46004 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.6 % / Rsym value: 0.075 / Net I/σ(I): 34.24 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 2252 / Rsym value: 0.605 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.658→29.22 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.52 / 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: 1.658→29.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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