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- PDB-1n4v: ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @pH 5.8 (STREP... -

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Basic information

Entry
Database: PDB / ID: 1n4v
TitleATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @pH 5.8 (STREPTOMYCES SP. SA-COO)
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / 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
: / GMC oxidoreductase, C-terminal / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain ...: / GMC oxidoreductase, C-terminal / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsVrielink, A. / Lario, P.I.
CitationJournal: 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
DepositionNov 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholesterol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8473
Polymers54,9701
Non-polymers8782
Water13,313739
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.354, 73.291, 63.171
Angle α, β, γ (deg.)90.00, 105.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholesterol oxidase / CHOD


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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 41.07 %
Crystal growpH: 5.8 / Details: PEG 8000, MANGANESE SULFATE, CACODYLATE, pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 1999
RadiationMonochromator: CRYSTALS SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1→46.9 Å / Num. obs: 230865 / % possible obs: 95 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.2
Reflection shellResolution: 1→1.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.7 / % possible all: 90.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: 1MXT

1mxt


Resolution: 1→46.9 Å / Num. parameters: 45907 / Num. restraintsaints: 61411 / 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.; RESI 396 CZ -> END IS MISSING.; RES 436 CG->END IS MISSING; PARTIALLY OCCUPIED SIDE CHAIN ATOMS MODELED AT 50% OR THE FOLLOWING: RES 73 ATOMS CD OE1 OE2; RES 127 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 145 ATOMS CGOD1 OD2; 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 180 ATOMS CG 1HG 2HG CD OE1 NE2 1HE2 2HE2; 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 396 ATOMS NE HE; RES 435 ATOMS CB HB OG1 CG2 1HG2 2HG2 3HG2; RES 436 ATOMS CB 1HB 2HB; RES 468 ATOMS NZ 1HZ 2HZ 3HZ;
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 11553 5 %RANDOM
Rwork0.1189 ---
all0.1196 230858 --
obs-230858 95 %-
Refine analyzeNum. disordered residues: 105 / Occupancy sum hydrogen: 3742.94 / Occupancy sum non hydrogen: 4435.02
Refinement stepCycle: LAST / Resolution: 1→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 59 739 4619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0339
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.082

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