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Yorodumi- PDB-1n4u: CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n4u | ||||||
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Title | CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. SA-COO) | ||||||
Components | Cholesterol oxidase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM / ATOMIC RESOLUTION | ||||||
Function / homology | Function and homology information 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 | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å | ||||||
Authors | Vrielink, A. / Lario, P.I. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n4u.cif.gz | 344.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n4u.ent.gz | 280.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n4u ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n4u | HTTPS FTP |
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-Related structure data
Related structure data | 1n4vC 1n4wC 2gewC 1mxtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: CHOA / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P12676, cholesterol oxidase |
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-Non-polymers , 5 types, 707 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 |
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 |
-Processing
Software |
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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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