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- PDB-1n4u: CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n4u | ||||||
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Title | CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (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 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 | ![]() | 344.2 KB | Display | ![]() |
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PDB format | ![]() | 280.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.8 KB | Display | ![]() |
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Full document | ![]() | 500.4 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n4vC ![]() 1n4wC ![]() 2gewC ![]() 1mxtS C: citing same article ( 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 707 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/FAE.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAE.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-FAE / | #4: Chemical | ChemComp-OXY / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.1 % |
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Crystal grow | pH: 4.5 / Details: pH 4.5 |
-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→46.8 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: 3.09 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.49 / % possible all: 89.3 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: 1MXT Resolution: 0.95→46.9 Å / Num. parameters: 45412 / Num. restraintsaints: 60231 / 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 278 CG -> END IS MISSING.; RES 396 CZ->END IS MISSING.; RES 436 CG->END IS MISSING; PARTIALLY OCCUPIED SIDE CHAIN ATOMS MODELED AT 50% FOR THE FOLLOWING: RES 73 ATOMS CG 1HG1 2HG CD OE1 OE2; RESI 127 ATOMS CG 1HD 2HD NE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES RES 163 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 172 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 183 CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 241 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 396 CG 1HG 2HG CD 1HD 2HD NE 1HE 2HE ; RES 398 CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 435 ATOMS CB HB OG1 CG2 1HG2 2HG2 3HG2; RES 436 ATOMS CB 1HB 2HB; RES 468 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ;
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Refine analyze | Num. disordered residues: 98 / Occupancy sum hydrogen: 3708.35 / Occupancy sum non hydrogen: 4437.13 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→46.9 Å
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Refine LS restraints |
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