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Yorodumi- PDB-4kia: Crystal structure of LmHde, heme-degrading enzyme, from Listeria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kia | ||||||
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Title | Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes | ||||||
Components | Lmo2213 protein | ||||||
Keywords | OXIDOREDUCTASE / ferredoxin fold / Heme-degrading enzyme / Heme binding | ||||||
Function / homology | ABM domain profile. / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Lmo2213 protein Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kim, K.K. / Duong, T. / Kim, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes. Authors: Duong, T. / Park, K. / Kim, T. / Kang, S.W. / Hahn, M.J. / Hahn, M.J. / Hwang, H.Y. / Jang, I. / Oh, H.B. / Kim, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kia.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kia.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kia_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 4kia_full_validation.pdf.gz | 417.2 KB | Display | |
Data in XML | 4kia_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4kia_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/4kia ftp://data.pdbj.org/pub/pdb/validation_reports/ki/4kia | HTTPS FTP |
-Related structure data
Related structure data | 3fezS S: Starting model for refinement |
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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: 19771.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2213 / Plasmid: pvFT1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y563 |
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#2: 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: 1.81 Å3/Da / Density % sol: 32.14 % |
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Crystal grow | Temperature: 287 K / Method: microbatch / pH: 5.6 Details: 25% PEG 3350, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 5.6, MICROBATCH, temperature 287K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 14344 / Num. obs: 14209 / % possible obs: 99 % / Redundancy: 3.6 % / Rsym value: 0.064 / Net I/σ(I): 30.41 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 5.78 / Rsym value: 0.166 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FEZ Resolution: 1.75→45.29 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.742 / SU ML: 0.085 / Cross valid method: COOT and PROCHECK / ESU R: 0.339 / ESU R Free: 0.138 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.794 Å / Total num. of bins used: 20
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