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- PDB-1n1p: ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (STRE... -

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Basic information

Entry
Database: PDB / ID: 1n1p
TitleATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (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: 0.95 Å
AuthorsVrielink, A. / Lario, P.I.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Atomic Resolution Density Maps Reveal Secondary Structure Dependent Differences in Electronic Distribution
Authors: Lario, P.I. / Vrielink, A.
History
DepositionOct 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)56,0126
Polymers54,9701
Non-polymers1,0425
Water14,736818
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.273, 72.964, 63.036
Angle α, β, γ (deg.)90.00, 105.18, 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


Mass: 18.015 Da / Num. of mol.: 818 / 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: 1.71 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 8000, MANGANESE SULFATE,GLYCINE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 %PEG MW 80001reservoir
275 mM1reservoirMnSO4
3100 mMglycine1reservoirpH9.0

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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 / Detector: CCD / Date: Aug 26, 1999
RadiationMonochromator: CRYST / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.95→49 Å / Num. obs: 277783 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.4
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. unique all: 18424 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 2567129
Reflection shell
*PLUS
% possible obs: 98.8 % / Mean I/σ(I) obs: 2.22

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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: 0.95→49 Å / Num. parameters: 46576 / Num. restraintsaints: 61542 / 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.; RES 241 NZ 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 127 ATOMS CG 1HG 2HG CE 1HE 2HE NZ 1HZ 2HZ 3H; RES 145 ATOMS CD OD1 OD2; RES 146 ATOMS NE 1HE; 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 183 ATOMS CD 1HD 2HD; RES 241 ATOMS CE 1HE 2HE; RES 396 ATOMS CD 1HD 2HD NE HE CZ NH1 1HH1 2HH1 NH2 1HH2 2HH2;
RfactorNum. reflection% reflectionSelection details
Rfree0.1189 12008 5 %RANDOM
Rwork0.0966 ---
all0.0971 239945 --
obs-239945 98.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 118 / Occupancy sum hydrogen: 3739.97 / Occupancy sum non hydrogen: 4483.32
Refinement stepCycle: LAST / Resolution: 0.95→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 62 818 4704
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_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.08
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.119 / Rfactor Rwork: 0.097
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.034
X-RAY DIFFRACTIONs_chiral_restr0.1

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