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4rek

Crystal structure and charge density studies of cholesterol oxidase from Brevibacterium sterolicum at 0.74 ultra-high resolution

Method: X-RAY DIFFRACTION Dmax: 77.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cholesterol oxidase

Streptomyces sp.

UniProt P12676

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 46–544 Fragment：UNP residues 64-544 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；290.15 K；The crystallization solution was composed of 9-11% poly(ethylene glycol) (PEG) MW 8000, 75mM MnSO4 and 100mM sodium cacodylate buffer., pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K Resolution 0.74 Å R-free 0.123

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4REK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B4V CHOLESTEROL OXIDASE FROM STREPTOMYCES Deposited 1998-12-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PRECIPITANT CONDITIONS: 10- 12% PEG 8000, 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML, VAPOR DIFFUSION, HANGING DROP
Resolution 1.50 Å R-free 0.200
1B8S CHOLESTEROL OXIDASE FROM STREPTOMYCES GLU361GLN MUTANT Deposited 1999-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–536（491 aa）
Mutation：GLU361GLN FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PRECIPITANT CONDITIONS: 10-12% PEG 8000, 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML , VAPOR DIFFUSION, HANGING DROP
Resolution 1.65 Å R-free 0.231
1CBO CHOLESTEROL OXIDASE FROM STREPTOMYCES HIS447ASN MUTANT Deposited 1999-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：H447N FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.2；CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION USING THE HANGING DROP TECHNIQUE, PRECIPITANT CONDITIONS: 10-12% PEG 8000, 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML
Resolution 1.80 Å R-free 0.194
1CC2 CHOLESTEROL OXIDASE FROM STREPTOMYCES HIS447GLN MUTANT Deposited 1999-03-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：H447Q FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.2；CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION USING THE HANGING DROP TECHNIQUE, PRECIPITANT CONDITIONS: 10-12% PEG 8000 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML
Resolution 2.20 Å R-free 0.235
1IJH CHOLESTEROL OXIDASE FROM STREPTOMYCES ASN485LEU MUTANT Deposited 2001-04-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：N485L FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；290 K；PEG 8000, SODIUM CACODYLATE, MNSO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.53 Å R-free 0.213
1MXT Atomic resolution structure of Cholesterol oxidase (Streptomyces sp. SA-COO) Deposited 2002-10-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded SO4 SULFATE ION × 1 FAE FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE × 1 OXY OXYGEN MOLECULE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；PEG 8000, manganese sulfate, cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 0.95 Å R-free 0.132
1N1P ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (STREPTOMYCES SP. SA-COO) Deposited 2002-10-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded MN MANGANESE (II) ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；PEG 8000, MANGANESE SULFATE,GLYCINE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 0.95 Å R-free 0.119
1N4U CHOLESTEROL OXIDASE FROM STREPTOMYCES @ pH 4.5 (STREPTOMYCES SP. SA-COO) Deposited 2002-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded PO4 PHOSPHATE ION × 5 FAE FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE × 1 OXY OXYGEN MOLECULE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 0.95 Å R-free 0.136
1N4V ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @pH 5.8 (STREPTOMYCES SP. SA-COO) Deposited 2002-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；PEG 8000, MANGANESE SULFATE, CACODYLATE, pH 5.8
Resolution 1.00 Å R-free 0.147
1N4W ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.3 (STREPTOMYCES SP. SA-COO) Deposited 2002-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded MN MANGANESE (II) ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；PEG 8000, MANGANESE SULFATE, MES, pH 7.3
Resolution 0.92 Å R-free 0.122
2GEW Atomic resolution structure of cholesterol oxidase @ pH 9.0 (Streptomyces sp. SA-COO) Deposited 2006-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded SO4 SULFATE ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 OXY OXYGEN MOLECULE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 8000, AMMONIUM SULFATE, PIPES PH 7.5,VAPOR DIFFUSION, HANGING DROP, temperature 298K, SOAK CONDITION STEP 1: PEG 8000, AMMONIUM SULFATE, HEPES PH 8.0 SOAK CONDITION STEP 2: PEG 8000, AMMONIUM SULFATE, TRICINE PH 8.5 SOAK CONDITION STEP 3: PEG 8000, AMMONIUM SULFATE, CHES PH 9.0,
Resolution 0.97 Å R-free 0.140
3B3R Crystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A) Deposited 2007-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–546（505 aa）
Mutation：E361Q/H447Q SO4 SULFATE ION × 2 FAE FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；10% PEG 8000, 75mM magnesium sulfate, 100mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 0.98 Å R-free 0.159
3B6D Crystal Structure of Streptomyces Cholesterol Oxidase H447Q/E361Q mutant (1.2A) Deposited 2007-10-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：H447Q/E361Q SO4 SULFATE ION × 1 FAE FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；10% PEG 8000, 75mM MnSO4, 100mM CACODYLATE pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.20 Å R-free 0.172
3CNJ Cholesterol oxidase from Streptomyces sp. F359W mutant (0.95A) Deposited 2008-03-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 45–543（499 aa）
Mutation：F359W SO4 SULFATE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；PEG 8000, MANGANESE SULFATE, CACODYLATE (PH 5.2), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 0.95 Å R-free 0.175
3GYI Cholesterol oxidase from Streptomyces sp. N485D mutant (1.0A) Deposited 2009-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：N485D FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；9-11% PEG 8000, 75 mM MnSO4, 100 mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.00 Å R-free 0.158
3GYJ Cholesterol oxidase from Streptomyces sp. N485L mutant (0.92A) Deposited 2009-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Mutation：N485L FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；9-11% PEG 8000, 75 mM MnSO4, 100 mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 0.92 Å R-free 0.151
4U2L Dithionite reduced cholesterol in complex with sulfite Deposited 2014-07-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded SO4 SULFATE ION × 3 SFD (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 8000, manganese chloride, cacodylate
Resolution 1.34 Å R-free 0.133
4U2S Cholesterol oxidase in the reduced state complexed with isopropanol Deposited 2014-07-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded SO4 SULFATE ION × 4 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8000, manganese sulfate, cacodylate
Resolution 1.12 Å R-free 0.107
4U2T Cholesterol oxidase in the oxidised state complexed with isopropanol Deposited 2014-07-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded SO4 SULFATE ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8000, manganese sulfate, cacodylate
Resolution 1.22 Å R-free 0.149
4XWR X-ray structure of perdeuterated Cholesterol Oxidase from Streptomyces SA-COO Deposited 2015-01-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；293 K；PEG 8K, MnSO4, sodium cacodylate
Resolution 1.10 Å R-free 0.107
4XXG Structure of protonated Cholesterol Oxidase from Streptomyces SA-COO Deposited 2015-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8K, MnSO4, sodium cacodylate
Resolution 0.85 Å R-free 0.124
5KWF Joint X-ray Neutron Structure of Cholesterol Oxidase Deposited 2016-07-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–546（504 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 Experimental method not declared
X-ray crystallization conditions VAPOR DIFFUSION；293 K；7% PEG 8000, 100mM MnSO4, 100mM cacodylic acid pH 5.2
Resolution not provided

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHOD_STRS0
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–499； UniProt 46–544

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4rek

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rek
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rek
Deposition date deposition_date2014-09-23
Structure title titleCrystal structure and charge density studies of cholesterol oxidase from Brevibacterium sterolicum at 0.74 ultra-high resolution
Keywords keywordsOxidase, FAD Binding, Membrane, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.92 Å
Radius of gyration Rg (electron density) rg_electron21.87 Å
Forward intensity I(0) i051932200.00
Molecular weight molecular_weight55246.0 kDa
Excluded volume excluded_volume68669 ų
Envelope volume envelope_volume76616 ų
Hydration-shell volume shell_volume28298 ų
Envelope diameter envelope_diameter78.7 Å
Shell Rg shell_rg29.65 Å
Envelope Rg envelope_rg22.03 Å
Shape Rg shape_rg21.86 Å
Total Rg total_rg22.72 Å
Total atoms total_atoms7673
Residues n_residues499
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.6 Å
Rg (real space) rg_real22.80 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real5.1930e+07
I(0) uncertainty (real space) i0_real_error7.3470e+05
Rg (reciprocal space) rg_reciprocal22.83 Å
I(0) (reciprocal space) i0_reciprocal51930000.0000
Solution quality estimate total_estimate0.8684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6 Å
Skewness Skewness skewness0.219
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha13270000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4rekA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id4rekA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily10 — Cholesterol Oxidase; domain 2
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8. Citations (1)

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9. Files and Curves (10)