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Yorodumi- PDB-1i9c: GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i9c | ||||||
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Title | GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE | ||||||
Components | (GLUTAMATE MUTASE) x 2 | ||||||
Keywords | ISOMERASE / COENZYME B12 / RADICAL REACTION / RIBOSE PSEUDOROTATION / TIM-BARREL / ROSSMAN-FOLD | ||||||
Function / homology | Function and homology information methylaspartate mutase / anaerobic glutamate catabolic process / methylaspartate mutase activity / glutamate catabolic process via L-citramalate / cobalamin binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium cochlearium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.9 Å | ||||||
Authors | Gruber, K. / Kratky, C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2001 Title: Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase Authors: Gruber, K. / Reitzer, R. / Kratky, C. #1: Journal: Structure / Year: 1999 Title: Glutamate Mutase from Clostridum Cochlearium: The Structure of a Coenzyme B12-Dependent Enzyme Provides New Mechanistic Insights Authors: Reitzer, R. / Gruber, K. / Jogl, G. / Wagner, U.G. / Bothe, H. / Buckel, W. / Kratky, C. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Analysis of Recombinant Glutamate Mutase and of the Isolated Component S from Clostridium Cochlearium Authors: Reitzer, R. / Krasser, M. / Jogl, G. / Buckel, W. / Bothe, H. / Kratky, C. #3: Journal: Eur.J.Biochem. / Year: 1994 Title: Characterization of the Coenzyme-B12-Dependent Glutamate Mutase from Clostridium Cochlearium Produced in Escherischia Coli Authors: Zelder, O. / Beatrix, B. / Leutbecher, U. / Buckel, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i9c.cif.gz | 293.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i9c.ent.gz | 230.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i9c_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1i9c_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1i9c_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 1i9c_validation.cif.gz | 90.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9c ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9c | HTTPS FTP |
-Related structure data
Related structure data | 1ccwS 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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Details | The biological assembly is the heterotetramer present in the asymmetric unit |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14830.991 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLMS / Plasmid: POZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: P80078, methylaspartate mutase #2: Protein | Mass: 53623.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH ADENOSYLCOBALAMAIN AND A MIXTURE OF GLUTAMATE AND 2S,3S-3-METHYLASPARTIC ACID Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLME / Plasmid: POZ5 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P80077, methylaspartate mutase |
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-Non-polymers , 5 types, 1266 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.4 Å3/Da / Density % sol: 48.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: PEG-4000, cadmium chloride, coenzyme B12, sodium glutamate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8439 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 121680 / Num. obs: 121680 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5 / Num. unique all: 8102 / Rsym value: 0.281 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 555148 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 8102 / Num. measured obs: 30037 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1CCW Resolution: 1.9→30 Å / Num. parameters: 45086 / Num. restraintsaints: 56174 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.3 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 39 / Occupancy sum hydrogen: 9804 / Occupancy sum non hydrogen: 11102 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.168 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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