+Open data
-Basic information
Entry | Database: PDB / ID: 1e1c | ||||||
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Title | METHYLMALONYL-COA MUTASE H244A Mutant | ||||||
Components |
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Keywords | ISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE | ||||||
Function / homology | Function and homology information lactate fermentation to propionate and acetate / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Evans, P.R. / Thoma, N.H. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Protection of Radical Intermediates at the Active Site of Adenosylcobalamin-Dependent Methylmalonyl-Coa Mutase Authors: Thoma, N.H. / Evans, P.R. / Leadlay, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1c.cif.gz | 575.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1c.ent.gz | 452.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e1c_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1e1c_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1e1c_validation.xml.gz | 131.4 KB | Display | |
Data in CIF | 1e1c_validation.cif.gz | 181.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1c ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1c | HTTPS FTP |
-Related structure data
Related structure data | 1reqS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999851, 0.00324, -0.01696), Vector: Details | BIOLOGICAL UNIT : HETERODIMERTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWOHETERODIMERIC MOLECULES , EACH WITH AN ALPHA CHAIN(CHAINS A AND C, CORRESPONDING TO GENE MUTB) AND A BETACHAIN ( CHAINS B AND D, CORRESPONDING TO GENE MUTA). MOLECULE 1 CONSISTS OF CHAINS A (ALPHA), B (BETA ), WITHWATERS X. MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D(BETA), WATERS Y. CHAINS A AND C INCLUDE COENZYME B12(RESIDUE 800), DESULPHO-COA ( RESIDUE 801) | |
-Components
#1: Protein | Mass: 80070.781 Da / Num. of mol.: 2 / Fragment: WHOLE MOLECULE / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHAINS A AND C INCLUDE COENZYME B12, AND DESULPHO-COA. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R Source: (gene. exp.) PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria) Strain: NCIB 9885 / Plasmid: PGP1-2, PMEX1 / Gene (production host): MUTA, MUTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K38 / References: UniProt: P11653, methylmalonyl-CoA mutase #2: Protein | Mass: 69430.188 Da / Num. of mol.: 2 / Fragment: WHOLE MOLECULE Source method: isolated from a genetically manipulated source Source: (gene. exp.) PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria) Strain: NCIB 9885 Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID Plasmid: PGP1-2, PMEX1 / Gene (production host): MUTA, MUTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K38 / References: UniProt: P11652, methylmalonyl-CoA mutase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CHAIN A AND C ENGINEERED MUTATION HIS244ALA THIS STRUCTURE IS OF THE HIS244 - ALA MUTANT IN THE ...CHAIN A AND C ENGINEERED | Sequence details | THE SEQUENCES IN THE SWISSPROT DATABASE (MUTB, ALPHA CHAIN AND MUTA, ALPHA CHAIN) CONTAIN N- ...THE SEQUENCES IN THE SWISSPROT DATABASE (MUTB, ALPHA CHAIN AND MUTA, ALPHA CHAIN) CONTAIN N-TERMINAL METHIONINE | |
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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: 2.83 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 14.4% PEG 4000, 20% V/V GLYCEROL, 12MM DESULPHO-COA, ADENOSYLCOBALAMIN 16MM,TRIS/HCL 100 MM, PH 7.5 THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME ...Details: 14.4% PEG 4000, 20% V/V GLYCEROL, 12MM DESULPHO-COA, ADENOSYLCOBALAMIN 16MM,TRIS/HCL 100 MM, PH 7.5 THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME B12) AND 12MM DESULPHO-COA (FINAL CONCENTRATIONS), EQUILIBRATED AGAINST 14% W/V PEG 4000 AND 20% V/V GLYCEROL, 100MM TRIS PH 7.5. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop / Details: Mancia, F., (1999) Biochemitry, 38, 7999. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→29 Å / Num. obs: 335799 / % possible obs: 97.1 % / Observed criterion σ(I): 6 / Redundancy: 3.4 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.62→2.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.446 / % possible all: 97.1 |
Reflection | *PLUS Num. obs: 99776 / Num. measured all: 335799 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1REQ Resolution: 2.62→29.2 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→29.2 Å
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Refine LS restraints |
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