+Open data
-Basic information
Entry | Database: PDB / ID: 3eiw | ||||||
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Title | Crystal structure of Staphylococcus aureus lipoprotein, HtsA | ||||||
Components | HtsA protein | ||||||
Keywords | TRANSPORT PROTEIN / siderophore / lipoprotein / heme / haem | ||||||
Function / homology | Function and homology information ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Grigg, J.C. / Murphy, M.E.P. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2009 Title: Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus. Authors: Beasley, F.C. / Vines, E.D. / Grigg, J.C. / Zheng, Q. / Liu, S. / Lajoie, G.A. / Murphy, M.E. / Heinrichs, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eiw.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eiw.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3eiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eiw_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 3eiw_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 3eiw_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3eiw_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/3eiw ftp://data.pdbj.org/pub/pdb/validation_reports/ei/3eiw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33359.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His6-tag Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: N315 / Gene: htsA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99S89, UniProt: A0A0H3JM89*PLUS |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 Hepes pH 7.0, Jeffamine ED-2001, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2007 Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: a double crystal monochromator (DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal, and vertically focussing mirror (VFM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 36952 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.809 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.399 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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