+Open data
-Basic information
Entry | Database: PDB / ID: 5b51 | ||||||
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Title | Crystal structure of heme binding protein HmuT R242A mutant | ||||||
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: 1.3 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 | 5b51.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b51.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 5b51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b51_validation.pdf.gz | 817.3 KB | Display | wwPDB validaton report |
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Full document | 5b51_full_validation.pdf.gz | 819 KB | Display | |
Data in XML | 5b51_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 5b51_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b51 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b51 | HTTPS FTP |
-Related structure data
Related structure data | 5b4zC 5b50C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36061.109 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359 / Mutation: R242A 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: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.90 M Ammonium sulfate, 0.19 M Ammonium tartrate, 0.16 M Potassium thiocyanate |
-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: Jun 29, 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: 1.3→48.68 Å / Num. obs: 96893 / % possible obs: 98.3 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.52 |
Reflection shell | Resolution: 1.3→1.34 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.58 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5az3 Resolution: 1.3→42.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.217 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / 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: 15.755 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→42.27 Å
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Refine LS restraints |
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