+Open data
-Basic information
Entry | Database: PDB / ID: 2qm8 | ||||||
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Title | MeaB, A Bacterial Homolog of MMAA, in the Nucleotide Free Form | ||||||
Components | GTPase/ATPase | ||||||
Keywords | CHAPERONE / G Protein / GTPase / G3E / Metallochaperone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Hubbard, P.A. / Padovani, D. / Labunska, T. / Mahlstedt, S.A. / Banerjee, R. / Drennan, C.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure and mutagenesis of the metallochaperone MeaB: insight into the causes of methylmalonic aciduria. Authors: Hubbard, P.A. / Padovani, D. / Labunska, T. / Mahlstedt, S.A. / Banerjee, R. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qm8.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qm8.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 2qm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qm8 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qm8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer which is contained within the asymmetric unit. |
-Components
#1: Protein | Mass: 35925.777 Da / Num. of mol.: 2 / Mutation: L192F, R224H, G257D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: meaB / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RPA0 #2: Chemical | ChemComp-PO4 / #3: 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: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris, pH 5.5, 0.2 M Li2SO4, and 17% PEG 3350., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2006 Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 78116 / Num. obs: 78116 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.071 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 7711 / Rsym value: 0.369 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MeaB Bound to GDP Resolution: 1.7→29.57 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.172 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å
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