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- PDB-1mxt: Atomic resolution structure of Cholesterol oxidase (Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 1mxt
TitleAtomic resolution structure of Cholesterol oxidase (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
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-N7 PROTONATED-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å
AuthorsVrielink, A. / Lario, P.I.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Sub-atomic resolution crystal structure of cholesterol oxidase: What atomic resolution crystallography reveals about enzyme mechanism and the role of FAD cofactor in redox activity
Authors: Lario, P.I. / Sampson, N. / Vrielink, A.
#1: 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
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / struct_conn / 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)55,8844
Polymers54,9701
Non-polymers9153
Water13,295738
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.227, 72.902, 62.947
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) / Gene: CHOA / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P12676, cholesterol oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAE / FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 786.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N9O15P2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 1.7 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, manganese sulfate, cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Details: Yue, Q.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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 / Wavelength: 0.979 Å
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: 0.95→28 Å / Num. obs: 266037 / % possible obs: 94.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.1
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 89.3
Reflection
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 28.2 Å / % possible obs: 94.1 % / Num. measured all: 1089496 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 88 %

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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: 1B4V

1b4v


Resolution: 0.95→28 Å / Num. parameters: 45239 / Num. restraintsaints: 59298 / 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 NE->END is missing.; RES 183 CE->END 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 87 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 127 ATOMS CG 1HG 2HG CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 156 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 163 ATOMS CG 1HG 2HG CD 1HD 2HD CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 183 ATOMS CG 1HG 2HG CD 1HD 2HD; 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 365 ATOMS CG 1HG 2HG SD CE 1HE 2HE 3HE; RES 396 ATOMS CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2; RES 398 ATOMS CE 1HE 2HE NZ 1HZ 2HZ 3HZ; RES 435 ATOMS CB HB OG1 CG2 1HG2 2HG2 3HG2; RES 436 ATOMS CB 1HB 2HB 3HB C; RES 468 ATOMS NZ 1HZ 2HZ 3HZ;
RfactorNum. reflection% reflectionSelection details
Rfree0.1318 13180 5 %RANDOM
Rwork0.11 ---
all0.1102 263551 --
obs0.0983 263551 94.1 %-
Refine analyzeNum. disordered residues: 82 / Occupancy sum hydrogen: 3697.86 / Occupancy sum non hydrogen: 4440.8
Refinement stepCycle: LAST / Resolution: 0.95→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 92 738 9221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0337
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.045
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.078
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28.2 Å / Num. reflection obs: 250371 / Rfactor Rfree: 0.132 / Rfactor Rwork: 0.11
Solvent computation
*PLUS
Displacement parameters
*PLUS

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