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- PDB-1mcz: BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mcz | |||||||||
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Title | BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE | |||||||||
![]() | BENZOYLFORMATE DECARBOXYLASE | |||||||||
![]() | LYASE / DECARBOXYLASE / THIAMIN DIPHOSPHATE / R-MANDELATE | |||||||||
Function / homology | ![]() benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Polovnikova, E.S. / Bera, A.K. / Hasson, M.S. | |||||||||
![]() | ![]() Title: Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase Authors: POLOVNIKOVA, E.S. / McLeish, M.J. / Sergienko, E.A. / Burgner, J.T. / Anderson, N.L. / BERA, A.K. / Jordan, F. / Kenyon, G.L. / HASSON, M.S. #1: ![]() Title: The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes Authors: Hasson, M.S. / Muscate, A. / McLeish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. | |||||||||
History |
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Remark 600 | HETEROGEN MG 529 (MAGNESIUM 2+) HAVE LOW B-FACTORS, SUGGESTING THAT THEY MAY ACTUALLY BE CALCIUM ...HETEROGEN MG 529 (MAGNESIUM 2+) HAVE LOW B-FACTORS, SUGGESTING THAT THEY MAY ACTUALLY BE CALCIUM IONS, AS IN STRUCTURE 1BFD. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 304.7 KB | Display | |
Data in CIF | ![]() | 409.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bfdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56402.746 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TPP / #4: Chemical | ChemComp-RMN / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R- ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: CuKa / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 561773 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 76.2 |
Reflection | *PLUS Num. obs: 206940 / % possible obs: 94 % / Num. measured all: 561773 |
Reflection shell | *PLUS % possible obs: 76 % / Rmerge(I) obs: 0.187 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BFD Resolution: 2.8→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: NCS restraints were used on all 16 monomers from residues 2-460 and 472-525. From 461-471, NCS restraints were also applied to two groups: (1) monomers A, D, F, G, H, K and N and (2) ...Details: NCS restraints were used on all 16 monomers from residues 2-460 and 472-525. From 461-471, NCS restraints were also applied to two groups: (1) monomers A, D, F, G, H, K and N and (2) monomers B, C, E, H, I, L, M, O and P. The side chains of two residues, Phe 464 and Trp 463, are in different conformations in the two groups. In 7 out of 8 cases, the two monomers that compose two active sites in the tetramer have opposite conformations from each other.
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.82 Å
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Refinement | *PLUS Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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