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- PDB-1ijh: CHOLESTEROL OXIDASE FROM STREPTOMYCES ASN485LEU MUTANT -

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Basic information

Entry
Database: PDB / ID: 1ijh
TitleCHOLESTEROL OXIDASE FROM STREPTOMYCES ASN485LEU MUTANT
ComponentsCHOLESTEROL OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM
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
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 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 / OTHER / Resolution: 1.53 Å
AuthorsVrielink, A. / Lario, P.I.
CitationJournal: Biochemistry / Year: 2001
Title: The presence of a hydrogen bond between asparagine 485 and the pi system of FAD modulates the redox potential in the reaction catalyzed by cholesterol oxidase.
Authors: Yin, Y. / Sampson, N.S. / Vrielink, A. / Lario, P.I.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)55,7542
Polymers54,9691
Non-polymers7861
Water10,935607
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.261, 72.881, 63.034
Angle α, β, γ (deg.)90.00, 105.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHOLESTEROL OXIDASE /


Mass: 54968.730 Da / Num. of mol.: 1 / Mutation: N485L
Source method: isolated from a genetically manipulated source
Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: choA / Plasmid: pCO237 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P12676, cholesterol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 8000, SODIUM CACODYLATE, MNSO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Details: Yue, K., (1999) Biochemistry, 38, 4277.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.5 mg/mlprotein1drop
210 mMHEPES1drop
310-12 %(w/v)PEG80001reservoir
4100 mMsodium cacodylate1reservoir
575 mM1reservoirMnSO4

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Data collection

DiffractionMean temperature: 86 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.52→25 Å / Num. obs: 63695 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.5
Reflection shellResolution: 1.52→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5048 / % possible all: 73.8
Reflection
*PLUS
Lowest resolution: 25 Å

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: OTHER
Starting model: 1B4V

1b4v


Resolution: 1.53→25 Å / Num. parameters: 18258 / Num. restraintsaints: 16261 / Cross valid method: FREE R / σ(F): 0 / σ(I): 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, ALA A 508, SER A 509. Some very mobile side chains were modeled at either 50% or ...Details: The following are residues that were not located in the experiment: ASP A 6, ASN A 7, GLY A 8, THR A 507, ALA A 508, SER A 509. Some very mobile side chains were modeled at either 50% or zero occupancy. The occupancy of absent side chain atoms was set to zero for the following: RES 396 ARG NE->end has zero occupancy. RES 436 GLN CG->end has zero occupancy. Partially occupied side chain atoms modeled at 50% for the following: RES 146 ARG atoms CZ, NH1,NH2; RES 163 LYS atoms CE,NZ; RES 273 LYS atoms CG,CD,CE,NZ; RES 278 LYS atoms CG,CD,CE,NZ; RES 279 GLU atoms CG,CD,OE1,OE2; RES 396 ARG atoms CG,CD (REST ZERO); RES 404 ASP atoms CG, OD1,OD2; RES 468 LYS atoms CG,CD,CE, NZ; Regarding the close contacts in remark 500: ARG 396 NH1 (zero occupancy); GLU 279 OE2 50% occupancy; ARG 202 NE very aniostropic B = 33; All of the flagged waters are modeled at 50% occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 63622 10 %RANDOM
Rwork0.1628 ---
all0.1655 68668 --
obs0.1655 63695 92.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 16.8 Å2
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4450.5
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 53 607 4560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 57331 / σ(F): 0 / Num. reflection Rfree: 6632 / % reflection Rfree: 10 % / Rfactor all: 0.166 / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.03

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