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- PDB-1mxt: Atomic resolution structure of Cholesterol oxidase (Streptomyces ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mxt | ||||||
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Title | Atomic resolution structure of Cholesterol oxidase (Streptomyces sp. SA-COO) | ||||||
![]() | CHOLESTEROL OXIDASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM / ATOMIC RESOLUTION | ||||||
Function / homology | ![]() cholesterol oxidase / cholesterol oxidase activity / steroid Delta-isomerase / steroid delta-isomerase activity / cholesterol catabolic process / flavin adenine dinucleotide binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vrielink, A. / Lario, P.I. | ||||||
![]() | ![]() Title: Sub-atomic resolution crystal structure of cholesterol oxidase: What atomic resolution crystallography reveals about enzyme mechanism and the role of FAD cofactor in redox activity Authors: Lario, P.I. / Sampson, N. / Vrielink, A. #1: ![]() Title: Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment Authors: Lyubimov, A.Y. / Lario, P.I. / Moustafa, I. / Vrielink, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.3 KB | Display | ![]() |
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PDB format | ![]() | 279.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.3 KB | Display | ![]() |
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Full document | ![]() | 486.2 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b4vS 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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Unit cell |
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Components
#1: Protein | Mass: 54969.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FAE / |
#4: Chemical | ChemComp-OXY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 40.39 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000, manganese sulfate, cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7 / Details: Yue, Q.K., (1999) Biochemistry, 38, 4277. | ||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 1999 |
Radiation | Monochromator: CRYSTALS SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→28 Å / Num. obs: 266037 / % possible obs: 94.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 89.3 |
Reflection | *PLUS Highest resolution: 0.95 Å / Lowest resolution: 28.2 Å / % possible obs: 94.1 % / Num. measured all: 1089496 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 88 % |
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Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: 1B4V Resolution: 0.95→28 Å / Num. parameters: 45239 / Num. restraintsaints: 59298 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE FOLLOWING ARE RESIDUES THAT WERE NOT LOCATED IN THE EXPERIMENT: ASP A 6, ASN A 7, GLY A 8, THR A 507 (only N was located), ALA A 508, SER A 509. SOME VERY MOBILE SIDE CHAINS WERE MODELED ...Details: THE FOLLOWING ARE RESIDUES THAT WERE NOT LOCATED IN THE EXPERIMENT: ASP A 6, ASN A 7, GLY A 8, THR A 507 (only N was located), ALA A 508, SER A 509. SOME VERY MOBILE SIDE CHAINS WERE MODELED AT EITHER 50% OR were not modelled. THE following atoms were not modelled: RES 146 NE->END is missing.; RES 183 CE->END is missing.; RES 436 CG->END is missing; PARTIALLY OCCUPIED SIDE CHAIN ATOMS MODELED AT 50% FOR THE FOLLOWING: RES 73 ATOMS CD OE1 OE2; RES 87 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 127 ATOMS CG 1HG 2HG CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 156 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 163 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 183 ATOMS CG 1HG 2HG CD 1HD 2HD; RES 241 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 273 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 365 ATOMS CG 1HG 2HG SD CE 1HE 2HE 3HE; RES 396 ATOMS CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 398 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 435 ATOMS CB HB OG1 CG2 1HG2 2HG2 3HG2; RES 436 ATOMS CB 1HB 2HB 3HB C; RES 468 ATOMS NZ 1HZ 2HZ 3HZ;
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Refine analyze | Num. disordered residues: 82 / Occupancy sum hydrogen: 3697.86 / Occupancy sum non hydrogen: 4440.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→28 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28.2 Å / Num. reflection obs: 250371 / Rfactor Rfree: 0.132 / Rfactor Rwork: 0.11 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |