PDB-9ifd: OleP triple mutant F84Q/S240A/V291G in complex with LCA

ID or keywords:

Entry

Database: PDB / ID: 9ifd

Title

OleP triple mutant F84Q/S240A/V291G in complex with LCA

Components

Cytochrome P-450

Keywords

OXIDOREDUCTASE / Cytochrome P450 / epoxidase / lithocolic acid / mutant

Function / homology

Function and homology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function

Biological species

Streptomyces antibioticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Montemiglio, L.C. / Costanzo, A. / Fata, F. / Freda, I. / Demitri, N. / Savino, C. / Vallone, B. / Bulfaro, G. / Lardieri, A.

Funding support

1items

Citation

Journal: To Be Published
Title: OleP triple mutant F84Q/S240A/V291G in complex with LCA
Authors: Montemiglio, L.C. / Costanzo, A. / Fata, F. / Freda, I. / Demitri, N. / Savino, C. / Vallone, B. / Bulfaro, G. / Lardieri, A. / Di Renzo, M. / Barbizzi, L. / Amadei, M.

History

Deposition	Feb 18, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 2, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ifd.cif.gz	936.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ifd.ent.gz	790.3 KB	Display	PDB format
PDBx/mmJSON format	9ifd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/9ifd ftp://data.pdbj.org/pub/pdb/validation_reports/if/9ifd	HTTPS FTP

-
Related structure data

Related structure data	9ibm
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Cytochrome P-450

B: Cytochrome P-450

C: Cytochrome P-450

D: Cytochrome P-450

E: Cytochrome P-450

F: Cytochrome P-450

hetero molecules

280 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cytochrome P-450

hetero molecules

defined by author
Evidence: gel filtration
47.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cytochrome P-450

hetero molecules

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

3

C: Cytochrome P-450

hetero molecules

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

4

D: Cytochrome P-450

hetero molecules

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

5

E: Cytochrome P-450

hetero molecules

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

6

F: Cytochrome P-450

hetero molecules

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

Unit cell

Length a, b, c (Å)	248.041, 106.588, 163.731
Angle α, β, γ (deg.)	90.00, 131.27, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	SER	SER	A	A	9 - 406	12 - 409
2	1	THR	THR	SER	SER	B	B	9 - 406	12 - 409
1	2	ASP	ASP	SER	SER	A	A	12 - 406	15 - 409
2	2	ASP	ASP	SER	SER	C	C	12 - 406	15 - 409
1	3	ASP	ASP	SER	SER	A	A	12 - 406	15 - 409
2	3	ASP	ASP	SER	SER	D	D	12 - 406	15 - 409
1	4	VAL	VAL	SER	SER	A	A	14 - 406	17 - 409
2	4	VAL	VAL	SER	SER	E	E	14 - 406	17 - 409
1	5	ASP	ASP	SER	SER	A	A	12 - 406	15 - 409
2	5	ASP	ASP	SER	SER	F	F	12 - 406	15 - 409
1	6	ASP	ASP	SER	SER	B	B	12 - 406	15 - 409
2	6	ASP	ASP	SER	SER	C	C	12 - 406	15 - 409
1	7	ASP	ASP	SER	SER	B	B	12 - 406	15 - 409
2	7	ASP	ASP	SER	SER	D	D	12 - 406	15 - 409
1	8	VAL	VAL	SER	SER	B	B	14 - 406	17 - 409
2	8	VAL	VAL	SER	SER	E	E	14 - 406	17 - 409
1	9	ASP	ASP	SER	SER	B	B	12 - 406	15 - 409
2	9	ASP	ASP	SER	SER	F	F	12 - 406	15 - 409
1	10	ASP	ASP	TRP	TRP	C	C	12 - 407	15 - 410
2	10	ASP	ASP	TRP	TRP	D	D	12 - 407	15 - 410
1	11	VAL	VAL	SER	SER	C	C	14 - 406	17 - 409
2	11	VAL	VAL	SER	SER	E	E	14 - 406	17 - 409
1	12	ASP	ASP	TRP	TRP	C	C	12 - 407	15 - 410
2	12	ASP	ASP	TRP	TRP	F	F	12 - 407	15 - 410
1	13	VAL	VAL	SER	SER	D	D	14 - 406	17 - 409
2	13	VAL	VAL	SER	SER	E	E	14 - 406	17 - 409
1	14	ASP	ASP	TRP	TRP	D	D	12 - 407	15 - 410
2	14	ASP	ASP	TRP	TRP	F	F	12 - 407	15 - 410
1	15	VAL	VAL	SER	SER	E	E	14 - 406	17 - 409
2	15	VAL	VAL	SER	SER	F	F	14 - 406	17 - 409

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Cytochrome P-450 Mass: 45217.227 Da / Num. of mol.: 6 / Mutation: F84Q S240A V291G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819

-
Non-polymers , 5 types, 327 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-4OA / (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid / Lithocholic acid Mass: 376.573 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₃ / Comment: detergent*YM
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical	... ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.97 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 4.4 M sodium formate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→123.067 Å / Num. obs: 86958 / % possible obs: 85 % / Redundancy: 3.7 % / CC_1/2: 0.998 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.7→2.75 Å / Num. unique obs: 4465 / CC_1/2: 0.72

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→53.74 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / SU B: 25.617 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 1.009 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21857	4376	5 %	RANDOM
R_work	0.1873	-	-	-
obs	0.18888	82607	98.63 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 62.158 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	0.13 Å²
2-	-	-0.29 Å²	-0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→53.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18510	0	589	256	19355

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	19522
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	18479
X-RAY DIFFRACTION	r_angle_refined_deg	1.894	1.67	26631
X-RAY DIFFRACTION	r_angle_other_deg	1.319	1.588	42421
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.81	5	2382
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.383	20.337	1099
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.897	15	3044
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.424	15	210
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2500
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	22042
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	4486
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.94	3.313	9531
X-RAY DIFFRACTION	r_mcbond_other	1.94	3.314	9532
X-RAY DIFFRACTION	r_mcangle_it	3.018	4.974	11906
X-RAY DIFFRACTION	r_mcangle_other	3.018	4.974	11907
X-RAY DIFFRACTION	r_scbond_it	2.536	3.695	9991
X-RAY DIFFRACTION	r_scbond_other	2.389	3.654	9896
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.707	5.404	14724
X-RAY DIFFRACTION	r_long_range_B_refined	5.832	39.773	20646
X-RAY DIFFRACTION	r_long_range_B_other	5.827	39.742	20635
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12529	0.07
1	2	B	12529	0.07
2	1	A	12388	0.08
2	2	C	12388	0.08
3	1	A	12454	0.07
3	2	D	12454	0.07
4	1	A	12276	0.09
4	2	E	12276	0.09
5	1	A	12371	0.08
5	2	F	12371	0.08
6	1	B	12412	0.08
6	2	C	12412	0.08
7	1	B	12550	0.06
7	2	D	12550	0.06
8	1	B	12293	0.08
8	2	E	12293	0.08
9	1	B	12406	0.07
9	2	F	12406	0.07
10	1	C	12564	0.08
10	2	D	12564	0.08
11	1	C	12379	0.08
11	2	E	12379	0.08
12	1	C	12408	0.09
12	2	F	12408	0.09
13	1	D	12284	0.08
13	2	E	12284	0.08
14	1	D	12444	0.08
14	2	F	12444	0.08
15	1	E	12174	0.09
15	2	F	12174	0.09

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.33	307	-
R_work	0.311	6170	-
obs	-	-	100 %

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	2.9126	-1.1118	0.3463	2.2999	0.362	1.5871	-0.027	-0.2084	-0.0075	0.1427	0.0127	-0.1062	0.0814	-0.0883	0.0143	0.153	-0.052	0.015	0.1722	-0.0295	0.0156	43.8373	1.2594	10.3115
2	2.8055	1.2727	-0.2122	1.9909	-0.2291	1.5541	-0.0552	-0.0051	0.0215	-0.071	0.0013	-0.017	-0.0654	0.1882	0.0539	0.1586	-0.007	-0.0016	0.2576	0.1043	0.0575	26.3719	0.3296	50.7682
3	2.1356	-0.2095	-0.6212	1.1016	0.1303	3.6332	-0.0108	0.1593	-0.0617	-0.1213	-0.0374	0.0048	0.0105	-0.1631	0.0482	0.1132	0.0743	-0.045	0.079	-0.0634	0.1706	3.9325	27.9128	29.2506
4	1.8974	0.3071	0.0808	1.3684	-0.2924	3.3562	0.0014	-0.23	-0.05	0.1565	-0.148	-0.1894	-0.1509	0.1531	0.1466	0.1519	-0.132	-0.0951	0.1446	0.0729	0.2192	66.6322	27.1461	31.9206
5	1.9601	0.5359	0.0808	3.5249	-0.7106	1.4097	-0.0692	0.1883	-0.1281	-0.2226	0.0935	0.0451	0.1043	0.0002	-0.0243	0.3205	0.0128	-0.0315	0.3516	0.0212	0.3138	-17.1783	-35.3296	33.1903
6	2.3329	-1.1283	0.5664	2.9227	-0.875	1.4402	-0.0801	-0.5109	0.0496	0.3601	0.1665	0.2927	-0.1842	-0.4343	-0.0864	0.4501	-0.0557	-0.0274	0.5003	-0.0189	0.3327	87.8006	-40.1314	28.4733
7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.3658	0	0	0.3658	0	0.3658	0	0	0
8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.3658	0	0	0.3658	0	0.3658	0	0	0
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.3658	0	0	0.3658	0	0.3658	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 500
2	X-RAY DIFFRACTION	2	B	7 - 500
3	X-RAY DIFFRACTION	3	C	12 - 500
4	X-RAY DIFFRACTION	4	D	12 - 500
5	X-RAY DIFFRACTION	5	E	14 - 500
6	X-RAY DIFFRACTION	6	F	12 - 500

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 327 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 6 molecules ABCDEF

-Non-polymers , 5 types, 327 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 327 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi