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Yorodumi- PDB-4fkm: Structure of unliganded and reductively methylated FhuD2 from sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fkm | ||||||
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Title | Structure of unliganded and reductively methylated FhuD2 from staphylococcus aureus | ||||||
Components | Similar to ferric hydroxamate receptor 1 | ||||||
Keywords | METAL BINDING PROTEIN / Class III Solute Binding Protein / membrane protein / transport of hydroxamate siderophores / Reductive methylation of lysyl residues | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Podkowa, K.J. / Heinrichs, D.E. / Shilton, B.H. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Crystal and solution structure analysis of FhuD2 from Staphylococcus aureus in multiple unliganded conformations and bound to ferrioxamine-B. Authors: Podkowa, K.J. / Briere, L.A. / Heinrichs, D.E. / Shilton, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fkm.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fkm.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fkm_validation.pdf.gz | 476.1 KB | Display | wwPDB validaton report |
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Full document | 4fkm_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 4fkm_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 4fkm_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/4fkm ftp://data.pdbj.org/pub/pdb/validation_reports/fk/4fkm | HTTPS FTP |
-Related 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: 30878.389 Da / Num. of mol.: 2 / Fragment: UNP residues 44-301 Source method: isolated from a genetically manipulated source Details: expressed as GST fusion; GST removed using TEV protease Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAV2284 / Plasmid: pGEX-FhuD2(delta)43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99RY8, UniProt: A0A0H3JWU6*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10 mg/mL protein concentration; 20% (w/v) PEG 3350, 25% (w/v) PEG 400, 100 mM MgCl2,100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0000, 0.9797, 0.9795, 0.9793 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 21, 2005 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→60.3 Å / Num. all: 26093 / Num. obs: 26198 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.1 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.7 / Num. unique all: 3669 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→60 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→60 Å
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Refine LS restraints |
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