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Yorodumi- PDB-4lc1: MeaB, A Bacterial Homolog of MMAA, Bound to GDP and crystallized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lc1 | ||||||
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Title | MeaB, A Bacterial Homolog of MMAA, Bound to GDP and crystallized in the presence of GDP and [AlF4]- | ||||||
Components | Methylmalonyl-CoA mutase accessory protein | ||||||
Keywords | CHAPERONE / Alpha and beta protein / Metallochaperone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Koutmos, M. / Padovani, D. / Lofgren, M. / Banerjee, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Autoinhibition and Signaling by the Switch II Motif in the G-protein Chaperone of a Radical B12 Enzyme. Authors: Lofgren, M. / Koutmos, M. / Banerjee, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lc1.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lc1.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lc1 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lc1 | HTTPS FTP |
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-Related structure data
Related structure data | 2qm7S 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: 35597.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: meaB, MexAM1_META1p0188 / Plasmid: pET-21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5AP93 #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 % (w/v) PEG3350, and 0.2 M sodium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03262 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2008 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03262 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 60395 / Num. obs: 60064 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.43 / Num. unique all: 9832 / Rsym value: 0.403 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QM7 Resolution: 1.8→47.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.606 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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