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Yorodumi- PDB-6jsc: Crystal structure of the H434A variant of the C-terminal domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jsc | ||||||
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Title | Crystal structure of the H434A variant of the C-terminal domain of HtaA from Corynebacterium glutamicum | ||||||
Components | Hypothetical membrane protein | ||||||
Keywords | HEME-BINDING PROTEIN / heme / heme transport | ||||||
Function / homology | Htaa / Htaa / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Hypothetical membrane protein Function and homology information | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Muraki, N. / Aono, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria. Authors: Muraki, N. / Kitatsuji, C. / Okamoto, Y. / 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 | 6jsc.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jsc.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jsc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6jsc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6jsc_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6jsc_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/6jsc ftp://data.pdbj.org/pub/pdb/validation_reports/js/6jsc | HTTPS FTP |
-Related structure data
Related structure data | 6js9C 6jsaSC 6jsbC 6jsdC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18161.576 Da / Num. of mol.: 2 / Mutation: H434A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: Cgl0388 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NTB9 #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4.5 M HCOONA, HEPES pH7.0, 7% sucrose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 23, 2017 |
Radiation | Monochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→36.2 Å / Num. obs: 66461 / % possible obs: 98.19 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0665 / Rpim(I) all: 0.0263 / Rrim(I) all: 0.0716 / Net I/σ(I): 17.73 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.624 / Num. unique obs: 6437 / CC1/2: 0.884 / Rpim(I) all: 0.243 / Rrim(I) all: 0.67 / % possible all: 96.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JSA Resolution: 1.4→36.194 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→36.194 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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