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Open data
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Basic information
Entry | Database: PDB / ID: 7req | ||||||
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Title | METHYLMALONYL-COA MUTASE, 2-CARBOXYPROPYL-COA INHIBITOR COMPLEX | ||||||
![]() | (PROTEIN (METHYLMALONYL-COA ...) x 2 | ||||||
![]() | ISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evans, P.R. / Mancia, F. | ||||||
![]() | ![]() Title: Crystal structure of substrate complexes of methylmalonyl-CoA mutase. Authors: Mancia, F. / Smith, G.A. / Evans, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 565.2 KB | Display | ![]() |
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PDB format | ![]() | 447.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 111.3 KB | Display | |
Data in CIF | ![]() | 156.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6reqC ![]() 1reqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: (-0.518139, 0.062089, 0.85304), Vector: Details | THE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWO HETERODIMERIC MOLECULES, EACH WITH AN ALPHA CHAIN (CHAINS A AND C, CORRESPONDING TO GENE MUTB) AND A BETA CHAIN (CHAINS B AND D, CORRESPONDING TO GENE MUTA). MOLECULE 1 CONSISTS OF CHAINS A (ALPHA), B (BETA), WITH GLYCEROL (RESIDUES 3001 & 3002) AND WATERS (1-666). MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D (BETA), WITH GLYCEROL (RESIDUES 3003 & 3004) AND WATERS (667-1329). CHAINS A AND C INCLUDE COENZYME B12 (RESIDUES 1800 & 2800), AND THE INHIBITOR 2-CARBOXYPROPYL-COA (RESIDUE 1801 & 2801) | |
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Components
-PROTEIN (METHYLMALONYL-COA ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 80137.852 Da / Num. of mol.: 2 / Fragment: ALPHA-SUBUNIT Source method: isolated from a genetically manipulated source Details: ALPHA CHAINS A AND C INCLUDE COENZYME B12, AND THE INHIBITOR 2-CARBOXYPROPYL- COENZYME A. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R. Source: (gene. exp.) ![]() Species: Propionibacterium freudenreichii / Strain: NCIB 9885 Description: THE 2 GENES ARE COEXPRESSED FROM THE SAME PLASMID; Gene: MUTB / Plasmid: PMEX1 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTB / Production host: ![]() ![]() #2: Protein | Mass: 69430.188 Da / Num. of mol.: 2 / Fragment: BETA-SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Propionibacterium freudenreichii / Strain: NCIB 9885 Description: THE 2 GENES ARE COEXPRESSED FROM THE SAME PLASMID Gene: MUTA / Plasmid: PMEX1 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 1334 molecules ![](data/chem/img/2CP.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS ...THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRROR |
Radiation | Monochromator: DOUBLE SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 160294 / % possible obs: 97 % / Observed criterion σ(I): 3.5 / Redundancy: 4.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 6 / Rsym value: 0.165 / % possible all: 94 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 18 Å / Observed criterion σ(I): 3.5 / Redundancy: 4.5 % / Biso Wilson estimate: 32 Å2 |
Reflection shell | *PLUS % possible obs: 93.8 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1REQ Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Details: NCS RESTRAINTS BETWEEN TWO MOLECULES
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Displacement parameters | Biso mean: 26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |