+Open data
-Basic information
Entry | Database: PDB / ID: 5b50 | ||||||
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Title | Crystal structure of heme binding protein HmuT Y240A | ||||||
Components | ABC-type transporter, periplasmic component | ||||||
Keywords | TRANSPORT PROTEIN / Heme / ABC transporter | ||||||
Function / homology | : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / ABC-type transporter, periplasmic component Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Muraki, N. / Aono, S. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2016 Title: Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters Authors: Muraki, N. / Kitatsuji, C. / Ogura, M. / Uchida, T. / Ishimori, K. / Aono, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b50.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b50.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 5b50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b50_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5b50_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5b50_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5b50_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b50 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b50 | HTTPS FTP |
-Related structure data
Related structure data | 5b4zC 5b51C 5az3S 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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Unit cell |
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-Components
#1: Protein | Mass: 36055.129 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359 / Mutation: Y240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Strain: ATCC 13032 / Gene: Cgl0389 / Plasmid: pET22 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NTB8 |
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#2: Chemical | ChemComp-HEM / |
#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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.1 M Ammonium sulfate, 0.2 M Potassium thiocyanate, 0.5 % beta-Octyl glucoside, 20 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35.41 Å / Num. obs: 48329 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5az3 Resolution: 1.65→35.414 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3 / 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: 1.65→35.414 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.3743 Å / Origin y: 64.2685 Å / Origin z: 159.8299 Å
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Refinement TLS group | Selection details: all |