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- PDB-1n1p: ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (STRE... -
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Basic information
Entry | Database: PDB / ID: 1n1p | ||||||
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Title | ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (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: Atomic Resolution Density Maps Reveal Secondary Structure Dependent Differences in Electronic Distribution Authors: Lario, P.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 | ![]() | 352 KB | Display | ![]() |
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PDB format | ![]() | 287.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1mxtS 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 | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 40.56 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 8000, MANGANESE SULFATE,GLYCINE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion | ||||||||||||||||||||||||||||
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 / Detector: CCD / Date: Aug 26, 1999 |
Radiation | Monochromator: CRYST / 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→49 Å / Num. obs: 277783 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. unique all: 18424 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 2567129 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 2.22 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: 1MXT Resolution: 0.95→49 Å / Num. parameters: 46576 / Num. restraintsaints: 61542 / 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 CZ-> END IS MISSING.; RES 183 CD->END IS MISSING.; RES 241 NZ 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 127 ATOMS CG 1HG 2HG CE 1HE 2HE NZ 1HZ 2HZ 3H; RES 145 ATOMS CD OD1 OD2; RES 146 ATOMS NE 1HE; RES 156 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 163 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 183 ATOMS CD 1HD 2HD; RES 241 ATOMS CE 1HE 2HE; RES 396 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2;
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 118 / Occupancy sum hydrogen: 3739.97 / Occupancy sum non hydrogen: 4483.32 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→49 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.119 / Rfactor Rwork: 0.097 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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