PDB-5kwf: Joint X-ray Neutron Structure of Cholesterol Oxidase

ID or keywords:

Entry

Database: PDB / ID: 5kwf

Title

Joint X-ray Neutron Structure of Cholesterol Oxidase

Components

Cholesterol oxidase

Keywords

OXIDOREDUCTASE /

ISOMERASE

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

Biological species

Streptomyces sp. (bacteria)

Method

X-RAY DIFFRACTION /

NEUTRON DIFFRACTION / NUCLEAR REACTOR /

MOLECULAR REPLACEMENT / Resolution: 1.499 Å

Authors

Golden, E. / Vrielink, A. / Meilleur, F. / Blakeley, M.

Citation

Journal: Sci Rep / Year: 2017
Title: An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase.
Authors: Golden, E. / Yu, L.J. / Meilleur, F. / Blakeley, M.P. / Duff, A.P. / Karton, A. / Vrielink, A.

History

Deposition	Jul 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kwf.cif.gz	218.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5kwf.ent.gz	175.6 KB	Display	PDB format
PDBx/mmJSON format	5kwf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kw/5kwf ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kwf	HTTPS FTP

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Related structure data

Similar structure data	4rek-d 1b4v-d 1coy-d 1mxt-d 1n4w-d 3cnj-d 1cbo-d 4xxg-d 6bzq-3 1ijh-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#77 - May 2006 Glucose Oxidase similarity (5) #220 - Apr 2018 Dehalogenases similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #207 - Mar 2017 Photoactive Yellow Protein similarity (1) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Cholesterol oxidase

hetero molecules

56.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	51.605, 74.084, 63.828
Angle α, β, γ (deg.)	90.000, 105.210, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cholesterol oxidase / / CHOD / Cholesterol isomerase Mass: 55798.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (strain SA-COO) (bacteria) Strain: SA-COO / Gene: choA / Production host: Escherichia coli (E. coli) References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#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: Chemical	ChemComp-DOD / water / Heavy water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: D₂O

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION	1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 7% PEG 8000, 100mM MnSO4, 100mM cacodylic acid pH 5.2

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	293	1
2	293	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
NUCLEAR REACTOR	ORNL High Flux Isotope Reactor	CG4D		1	2.8-4.3
ROTATING ANODE			RIGAKU MICROMAX-007 HF	2	1.54

Detector

Type	ID	Detector	Date	Details
MAATEL IMAGINE	1	IMAGE PLATE	Jun 1, 2013
RIGAKU RAXIS IV++	2	IMAGE PLATE	Jul 1, 2013	Osmic Varimax

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	LAUE	L	neutron	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	2.8	1
2	4.3	1
3	1.54	1

Reflection

B_iso Wilson estimate: 12.4 Å² / Entry-ID: 5KWF

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	R_merge(I) obs	R_sym value	Diffraction-ID	Net I/av σ(I)	Net I/σ(I)
2.192-61.593	17714	76.7	4	0.258	0.258	1	2.471	4
1.499-40	67641	91.03	3.6			2		21.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.2-2.32	3.3	0.349	1.9	1	61.1
2.32-2.46	3.2	0.335	2.1	1	64.5
2.46-2.63	3.3	0.329	2.1	1	67.5
2.63-2.84	3.4	0.308	2.2	1	73
2.84-3.11	3.7	0.28	2.4	1	79.2
3.11-3.48	4.2	0.258	2.6	1	87.3
3.48-4.02	4.9	0.257	2.5	1	92.8
4.02-4.92	5.4	0.243	2.6	1	95
4.92-6.96	5.1	0.195	3.2	1	94.6
6.96-61.199	3.6	0.13	4.5	1	91.9

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

SU ML: 0.25 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.56 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Resolution (Å)	Refine-ID	B_iso max (Å²)	B_iso mean (Å²)	B_iso min (Å²)	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	Diffraction-ID	σ(F)
1.499-25.264	X-RAY DIFFRACTION	109.25	13.2196	0	0.2195	0.1904	0.1918	3376	67641	4.99	91.03	2	1.37
2.214-61.593	NEUTRON DIFFRACTION				0.3117	0.2835	0.2849	886	17713	5	76.21	1	0

Refinement step

Cycle: final / Resolution: 1.499→25.264 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3834	0	88	435	4357
B_iso mean	-	-	3.52	20.49	-
Num. residues	-	-	-	-	499

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	8825
X-RAY DIFFRACTION	f_angle_d	1.459	15612
X-RAY DIFFRACTION	f_chiral_restr	0.134	585
X-RAY DIFFRACTION	f_plane_restr	0.036	1788
X-RAY DIFFRACTION	f_dihedral_angle_d	23.11	2427

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	Num. reflection all	Total num. of bins used	% reflection obs (%)
2.2137-2.3523	0.3558	116	0.3531	2208	NEUTRON DIFFRACTION	2324	6	60
2.3523-2.534	0.3696	125	0.3309	2374	NEUTRON DIFFRACTION	2499	6	65
2.534-2.789	0.3288	135	0.3123	2566	NEUTRON DIFFRACTION	2701	6	70
2.789-3.1925	0.2609	153	0.2627	2883	NEUTRON DIFFRACTION	3036	6	78
3.1925-4.0222	0.278	172	0.2405	3285	NEUTRON DIFFRACTION	3457	6	89
4.0222-61.6169	0.3207	185	0.2705	3511	NEUTRON DIFFRACTION	3696	6	94
1.4991-1.5205	0.5266	131	0.5779	2477	X-RAY DIFFRACTION	2608	24	84
1.5205-1.5432	0.4268	132	0.5062	2506	X-RAY DIFFRACTION	2638	24	86
1.5432-1.5673	0.4205	133	0.3986	2537	X-RAY DIFFRACTION	2670	24	86
1.5673-1.593	0.2728	135	0.3134	2569	X-RAY DIFFRACTION	2704	24	88
1.593-1.6205	0.2419	136	0.2552	2578	X-RAY DIFFRACTION	2714	24	88
1.6205-1.6499	0.2242	137	0.2143	2602	X-RAY DIFFRACTION	2739	24	89
1.6499-1.6817	0.1987	138	0.1913	2637	X-RAY DIFFRACTION	2775	24	89
1.6817-1.716	0.1763	137	0.1682	2584	X-RAY DIFFRACTION	2721	24	88
1.716-1.7533	0.21	136	0.1494	2603	X-RAY DIFFRACTION	2739	24	90
1.7533-1.7941	0.1767	139	0.141	2620	X-RAY DIFFRACTION	2759	24	89
1.7941-1.8389	0.1903	140	0.1355	2655	X-RAY DIFFRACTION	2795	24	90
1.8389-1.8886	0.1706	139	0.1375	2636	X-RAY DIFFRACTION	2775	24	91
1.8886-1.9442	0.1668	141	0.1338	2687	X-RAY DIFFRACTION	2828	24	91
1.9442-2.0069	0.1769	142	0.1392	2704	X-RAY DIFFRACTION	2846	24	91
2.0069-2.0786	0.1981	143	0.1489	2702	X-RAY DIFFRACTION	2845	24	92
2.0786-2.1618	0.2086	142	0.1586	2704	X-RAY DIFFRACTION	2846	24	93
2.1618-2.2601	0.217	144	0.1581	2747	X-RAY DIFFRACTION	2891	24	93
2.2601-2.3792	0.2009	144	0.155	2755	X-RAY DIFFRACTION	2899	24	94
2.3792-2.5281	0.1837	140	0.1516	2768	X-RAY DIFFRACTION	2908	24	94
2.5281-2.7231	0.1895	148	0.1536	2792	X-RAY DIFFRACTION	2940	24	94
2.7231-2.9967	0.1881	149	0.1691	2798	X-RAY DIFFRACTION	2947	24	95
2.9967-3.4294	0.2057	149	0.1846	2849	X-RAY DIFFRACTION	2998	24	96
3.4294-4.3172	0.2088	151	0.1703	2854	X-RAY DIFFRACTION	3005	24	96
4.3172-25.2679	0.3096	150	0.2865	2901	X-RAY DIFFRACTION	3051	24	96

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