+Open data
-Basic information
Entry | Database: PDB / ID: 2qm7 | ||||||
---|---|---|---|---|---|---|---|
Title | MeaB, A Bacterial Homolog of MMAA, Bound to GDP | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.85 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qm7.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qm7.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qm7 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qm7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a homodimer which is contained within the asymmetric unit. |
-Components
#1: Protein | Mass: 35597.512 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.51 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 55277 / Num. obs: 55277 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.068 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.85→1.92 Å / Mean I/σ(I) obs: 10.5 / Num. unique all: 5028 / Rsym value: 0.214 / % possible all: 89.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Initial model derived from Se-Met derivative solved by MAD. Resolution: 1.85→29.92 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→29.92 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.902 Å
|