[English] 日本語
Yorodumi- PDB-2xiq: Crystal structure of human methylmalonyl-CoA mutase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xiq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin and malonyl-CoA | ||||||
Components | METHYLMALONYL-COA MUTASE, MITOCHONDRIAL | ||||||
Keywords | ISOMERASE / ORGANIC ACIDURIA / METABOLIC DISEASE / VITAMIN B12 | ||||||
Function / homology | Function and homology information succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process ...succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process / cobalamin binding / post-embryonic development / positive regulation of GTPase activity / mitochondrial matrix / GTPase activity / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Yue, W.W. / Froese, D.S. / Kochan, G. / Chaikuad, A. / Krojer, T. / Muniz, J. / Ugochukwu, E. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Yue, W.W. / Froese, D.S. / Kochan, G. / Chaikuad, A. / Krojer, T. / Muniz, J. / Ugochukwu, E. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation. Authors: Froese, D.S. / Kochan, G. / Muniz, J. / Wu, X. / Gileadi, C. / Ugochukwu, E. / Krysztofinska, E. / Gravel, R.A. / Oppermann, U. / Yue, W.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xiq.cif.gz | 590.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xiq.ent.gz | 486.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xiq ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xiq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2wwwC 2xijC 3bicSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 84835.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 12-750 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: P22033, methylmalonyl-CoA mutase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE |
---|---|
Crystal grow | Details: 20% PEG3350, 0.1 M BIS-TRIS PH 5.5, 0.1 M NH4-SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9824 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 9, 2010 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9824 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→53.91 Å / Num. obs: 129983 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BIC Resolution: 1.95→107.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.371 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.705 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→107.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|