PDB-4jbt: The 2.2 A crystal structure of CYP154C5 from Nocardia farcinica i...

ID or keywords:

Entry

Database: PDB / ID: 4jbt

Title

The 2.2 A crystal structure of CYP154C5 from Nocardia farcinica in complex with androstenedione

Components

Cytochrome P450 monooxygenase

Keywords

oxidoreductase/substrate / Cytochrom P450 / steroid hydroxylating monooxygenase / steroid binding / oxidoreductase-substrate complex

Function / homology

Function and homology information

cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function

Biological species

Nocardia farcinica (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Herzog, K. / Hoffmann, K.M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation.
Authors: Herzog, K. / Bracco, P. / Onoda, A. / Hayashi, T. / Hoffmann, K. / Schallmey, A.

History

Deposition	Feb 20, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jbt.cif.gz	326.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4jbt.ent.gz	279.2 KB	Display	PDB format
PDBx/mmJSON format	4jbt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jbt_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4jbt_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4jbt_validation.xml.gz	35.4 KB	Display
Data in CIF	4jbt_validation.cif.gz	49.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/4jbt ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jbt	HTTPS FTP

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Related structure data

Related structure data	4j6bC 4j6cC 4j6dC C: citing same article (ref.)
Similar structure data	4j6c-2 6zhz-6 4j6d-2 2zby-d 6to2-2 2zbx-d 4g48-d 1oxa-d 6to2-1 4wcx-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4j6bC

4j6cC

4j6dC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1)

Deposited unit

A: Cytochrome P450 monooxygenase

B: Cytochrome P450 monooxygenase

hetero molecules

92.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cytochrome P450 monooxygenase

hetero molecules

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

2

B: Cytochrome P450 monooxygenase

hetero molecules

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

3

B: Cytochrome P450 monooxygenase

hetero molecules

A: Cytochrome P450 monooxygenase

hetero molecules

defined by software
92.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.800, 102.800, 217.520
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

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Protein , 1 types, 2 molecules AB

#1: Protein	Cytochrome P450 monooxygenase Mass: 45376.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia farcinica (bacteria) / Strain: IFM 10152 / Gene: NFA_53110 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: Q5YNS8

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Non-polymers , 6 types, 334 molecules

#2: Chemical	ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₂₆O₂ / Comment: hormone*YM
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M MgCHO2 in the reservoir, condition mixed 1:1 from protein stock and reservoir, cocrystallisation with steroid , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2011

Radiation

Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.2→82.393 Å / Num. all: 40488 / Num. obs: 40488 / % possible obs: 93 % / Redundancy: 2.4 % / R_sym value: 0.076 / Net I/σ(I): 7.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.2-2.32	2.2	0.339	2.4	11875	5278	0.339	82.8
2.32-2.46	2.2	0.25	3.1	11263	5123	0.25	85
2.46-2.63	2.2	0.191	4	11463	5229	0.191	92.5
2.63-2.84	2.3	0.13	4.7	12033	5181	0.13	98.2
2.84-3.11	2.5	0.101	7.1	11743	4769	0.101	98.6
3.11-3.48	2.5	0.077	8.6	10715	4288	0.077	98.2
3.48-4.02	2.5	0.059	10.8	9516	3765	0.059	97.7
4.02-4.92	2.6	0.051	12.1	8137	3162	0.051	96.9
4.92-6.96	2.6	0.055	10.1	6311	2397	0.055	95.8
6.96-51.4	2.7	0.035	16	3470	1296	0.035	93.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.20	data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
MAR345dtb		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→51.4 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.915 / WR_factor R_free: 0.2447 / WR_factor R_work: 0.182 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.8636 / SU B: 9.406 / SU ML: 0.141 / SU R Cruickshank DPI: 0.0695 / SU R_free: 0.0507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2477	2020	5 %	RANDOM
R_work	0.1835	-	-	-
obs	0.1867	40105	92.08 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 108.52 Å² / B_iso mean: 35.4107 Å² / B_iso min: 11.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-21.63 Å²	-0 Å²	-0 Å²
2-	-	-21.63 Å²	-0 Å²
3-	-	-	43.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→51.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6268	0	145	321	6734

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	6559
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6296
X-RAY DIFFRACTION	r_angle_refined_deg	1.256	1.999	8979
X-RAY DIFFRACTION	r_angle_other_deg	0.73	3	14428
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.077	5	812
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.302	23.011	269
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.94	15	1037
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.473	15	57
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1041
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	7349
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1452
X-RAY DIFFRACTION	r_mcbond_it	2.046	2.098	3251
X-RAY DIFFRACTION	r_mcbond_other	2.046	2.098	3252
X-RAY DIFFRACTION	r_mcangle_it	2.95	3.139	4061

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
3811	MEDIUM POSITIONAL	0.08	0.5
2387	TIGHT THERMAL	1.81	0.5
3811	MEDIUM THERMAL	2.25	2

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	118	-
R_work	0.25	2359	-
all	-	2477	-
obs	-	-	76.93 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.1844	-2.2332	1.0589	1.1947	0.3757	3.2032	-0.1636	0.4148	0.5389	-0.1051	-0.2724	-0.1372	-0.6883	-0.345	0.436	0.2703	0.0411	0.0524	0.1283	0.0166	0.4128	34.337	15.759	9.318
2	2.2074	-0.5228	-0.1219	1.0374	-0.2047	1.4073	0.0874	-0.046	0.0939	0.0544	-0.0285	0.2839	-0.0179	-0.1926	-0.0589	0.059	0.0296	0.0522	0.0624	0.0145	0.2244	26.453	0.637	15.325
3	5.1596	0.5633	-1.1336	1.4827	-0.8265	1.2355	-0.0388	-0.8112	0.0283	0.3484	0.0187	0.0718	0.0982	0.0731	0.0201	0.2236	0.0325	-0.0002	0.1573	-0.0376	0.073	47.463	-11.072	27.893
4	34.5788	-16.5378	-3.4926	18.1613	4.7449	2.8019	-0.5722	-0.5536	-1.6542	0.2937	-0.1162	0.5204	0.5678	-0.1256	0.6884	0.2649	0.0856	0.117	0.1631	-0.1106	0.445	68.9	-4.943	10.854
5	1.5507	0.7841	0.0096	1.1893	-0.3327	0.2378	-0.054	0.1384	-0.121	-0.1645	0.0472	-0.1103	0.0522	0.0388	0.0068	0.0561	-0.0171	0.0136	0.052	-0.0249	0.0816	46.845	-10.48	9.353
6	8.9828	0.634	0.2841	7.3093	0.095	2.1764	0.1989	-0.4946	-0.5537	0.5927	-0.1764	0.0071	0.0483	0.0764	-0.0225	0.116	-0.0344	-0.0493	0.0755	0.0559	0.093	37.525	-23.591	24.112
7	1.1932	0.1859	-0.3573	1.3675	-0.081	0.7183	0.07	-0.1559	0.2343	0.1744	0.0172	-0.0823	-0.2194	-0.0052	-0.0872	0.1273	0.0196	0.0445	0.0613	-0.0276	0.0948	43.14	7.385	21.371
8	3.6804	-0.3355	-0.0999	0.8863	-0.1725	1.2886	0.01	-0.0665	0.4756	0.0864	0.0407	-0.0937	-0.2202	0.1533	-0.0508	0.0987	-0.0171	-0.0051	0.0312	-0.0399	0.1297	52.992	3.618	17.79
9	1.6165	3.1989	-0.4365	8.2588	0.757	1.4802	0.0221	-0.2185	-0.3749	0.5061	-0.294	-0.5507	0.3846	0.1745	0.272	0.2479	0.1078	-0.02	0.2256	-0.0243	0.2867	30.634	23.627	-5.047
10	1.6326	0.3786	-0.2827	1.4479	-0.0984	1.4555	-0.0284	0.0626	-0.394	-0.076	-0.0095	-0.0488	0.2452	-0.0171	0.0379	0.1306	0.0343	-0.002	0.0436	-0.0201	0.2362	16.356	22.013	-15.034
11	3.6773	4.06	1.5107	6.9248	2.777	2.1171	-0.1597	0.4355	-0.1219	-0.6138	0.2121	-0.116	-0.1062	-0.1295	-0.0524	0.1469	0.0409	0.0306	0.199	0.0122	0.0582	14.387	46.47	-28.07
12	17.8132	14.4754	2.5255	20.323	9.5665	32.3642	0.0274	-0.0737	0.6265	-0.1464	0.0302	0.4792	-1.0649	-0.1004	-0.0576	0.1642	0.0152	0.0293	0.0605	0.0612	0.0972	30.127	61.769	-10.633
13	1.9945	0.6041	0.5024	0.7452	-0.0172	0.6543	0.0306	-0.0468	0.2441	0.0147	-0.0255	0.0991	-0.0757	-0.0808	-0.0051	0.0609	0.0022	0.0473	0.0569	-0.0217	0.0907	11.516	46.212	-11.738
14	5.6453	0.4311	0.9631	1.4042	0.2301	0.6119	-0.0602	0.1667	0.2739	-0.2126	0.0018	0.1916	0.0532	0.0183	0.0584	0.1126	0.0064	0.0042	0.0702	-0.0073	0.0591	13.955	41.403	-20.144
15	18.9176	8.4138	-10.1984	3.7434	-4.538	5.5078	0.0377	-0.1578	-0.0959	0.027	-0.0946	-0.0622	-0.0797	0.0918	0.0569	0.3386	0.0001	0.0326	0.395	-0.0182	0.3349	42.745	47.27	-25.943
16	0.9059	0.4873	0.0517	2.0007	-0.1895	0.754	0.026	0.1531	-0.1949	-0.1189	-0.0099	-0.2114	0.0912	0.1382	-0.0162	0.0914	0.0817	0.0306	0.1375	-0.0404	0.0894	28.67	35.504	-19.643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 34
2	X-RAY DIFFRACTION	2	A	35 - 96
3	X-RAY DIFFRACTION	3	A	97 - 132
4	X-RAY DIFFRACTION	4	A	133 - 138
5	X-RAY DIFFRACTION	5	A	139 - 203
6	X-RAY DIFFRACTION	6	A	204 - 233
7	X-RAY DIFFRACTION	7	A	234 - 343
8	X-RAY DIFFRACTION	8	A	344 - 410
9	X-RAY DIFFRACTION	9	B	4 - 22
10	X-RAY DIFFRACTION	10	B	23 - 96
11	X-RAY DIFFRACTION	11	B	97 - 132
12	X-RAY DIFFRACTION	12	B	133 - 138
13	X-RAY DIFFRACTION	13	B	139 - 219
14	X-RAY DIFFRACTION	14	B	220 - 262
15	X-RAY DIFFRACTION	15	B	263 - 274
16	X-RAY DIFFRACTION	16	B	275 - 410

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