PDB-9ibm: OleP mutant F84Q in complex with LCA

ID or keywords:

Entry

Database: PDB / ID: 9ibm

Title

OleP mutant F84Q 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: 2.777 Å

Authors

Montemiglio, L.C. / Fata, F. / Costanzo, A. / Di Renzo, M. / Savino, C. / Vallone, B. / Bulfaro, G. / Barbizzi, L. / Lardieri, A.

Funding support

1items

Citation

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

History

Deposition	Feb 12, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ibm.cif.gz	945.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9ibm.ent.gz	794.6 KB	Display	PDB format
PDBx/mmJSON format	9ibm.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/ib/9ibm ftp://data.pdbj.org/pub/pdb/validation_reports/ib/9ibm	HTTPS FTP

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Related structure data

Similar structure data	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	#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

290 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
48.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cytochrome P-450

hetero molecules

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

3

C: Cytochrome P-450

hetero molecules

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

4

D: Cytochrome P-450

hetero molecules

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

5

E: Cytochrome P-450

hetero molecules

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

6

F: Cytochrome P-450

hetero molecules

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

Unit cell

Length a, b, c (Å)	250.060, 108.340, 162.120
Angle α, β, γ (deg.)	90.00, 129.95, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A1_	12 - 407
2	1	1	1	B4_	12 - 407
1	1	2	1	A1_	12 - 407
2	1	2	1	C7_	12 - 407
1	1	3	1	A1_	12 - 407
2	1	3	1	D0_	12 - 407
1	1	4	1	A1_	12 - 407
2	1	4	1	E0_	12 - 407
1	1	5	1	A1_	13 - 406
2	1	5	1	F0_	13 - 406
1	1	6	1	B4_	12 - 407
2	1	6	1	C7_	12 - 407
1	1	7	1	B4_	12 - 407
2	1	7	1	D0_	12 - 407
1	1	8	1	B4_	12 - 407
2	1	8	1	E0_	12 - 407
1	1	9	1	B4_	13 - 406
2	1	9	1	F0_	13 - 406
1	1	10	1	C7_	12 - 407
2	1	10	1	D0_	12 - 407
1	1	11	1	C7_	12 - 407
2	1	11	1	E0_	12 - 407
1	1	12	1	C7_	13 - 406
2	1	12	1	F0_	13 - 406
1	1	13	1	D0_	12 - 407
2	1	13	1	E0_	12 - 407
1	1	14	1	D0_	13 - 406
2	1	14	1	F0_	13 - 406
1	1	15	1	E0_	13 - 406
2	1	15	1	F0_	13 - 406

NCS ensembles :

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

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.999567, -0.028779, 0.006203), (-0.028388, 0.998037, 0.055826), (-0.007797, 0.055626, -0.998421)	72.97456, 2.27734, 63.25771

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Cytochrome P-450 Mass: 47164.371 Da / Num. of mol.: 6 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

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Non-polymers , 5 types, 227 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.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	... ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4.4 M sodium formate

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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: Mar 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.777→90 Å / Num. obs: 83589 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC_1/2: 0.996 / Net I/σ(I): 11.3
Reflection shell	Resolution: 2.777→2.825 Å / Num. unique obs: 4120 / CC_1/2: 0.819

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.777→61.72 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.926 / SU B: 29.328 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 1.457 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22834	4048	4.8 %	RANDOM
R_work	0.1828	-	-	-
obs	0.18503	79540	99.64 %	-

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: 65.167 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2 Å²	-0 Å²	-0.18 Å²
2-	-	-1.15 Å²	-0 Å²
3-	-	-	1.43 Å²

Refinement step

Cycle: 1 / Resolution: 2.777→61.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18919	0	86	184	19189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	19532
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	18516
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.863	26705
X-RAY DIFFRACTION	r_angle_other_deg	0.532	1.763	42522
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.401	5	2385
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.138	5	213
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.863	10	3064
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	3035
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	23365
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	4467
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	3.725	4.676	9522
X-RAY DIFFRACTION	r_mcbond_other	3.724	4.676	9523
X-RAY DIFFRACTION	r_mcangle_it	5.955	8.403	11901
X-RAY DIFFRACTION	r_mcangle_other	5.955	8.403	11902
X-RAY DIFFRACTION	r_scbond_it	4.291	5.104	10010
X-RAY DIFFRACTION	r_scbond_other	4.268	5.089	9953
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.009	9.151	14801
X-RAY DIFFRACTION	r_long_range_B_refined	11.279	44.49	21024
X-RAY DIFFRACTION	r_long_range_B_other	11.28	44.49	21023
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Number	Type	Rms dev position (Å)	Weight position
10	10	3084	tight positional	0.1	0.11
11	11	3084	tight positional	0.11	0.11
12	12	3061	tight positional	0.08	0.11
13	13	3092	tight positional	0.11	0.11
14	14	3069	tight positional	0.1	0.11
15	15	3061	tight positional	0.1	0.11
1	1	3115	tight thermal	4.43	1.12
2	2	3115	tight thermal	7.44	1.12
3	3	3115	tight thermal	6.73	1.12
4	4	3115	tight thermal	14.97	1.12
5	5	3092	tight thermal	15.07	1.12
6	6	3100	tight thermal	6.77	1.12
7	7	3100	tight thermal	6.17	1.12
8	8	3100	tight thermal	14.35	1.12
9	9	3077	tight thermal	14.59	1.12
10	10	3084	tight thermal	5.59	1.12
11	11	3084	tight thermal	14.24	1.12
12	12	3061	tight thermal	12.28	1.12
13	13	3092	tight thermal	12.35	1.12
14	14	3069	tight thermal	11.58	1.12
15	15	3061	tight thermal	11.05	1.12

LS refinement shell

Resolution: 2.777→2.849 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	267	-
R_work	0.297	5882	-
obs	-	-	99.69 %

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	0.8042	-0.0036	0.019	0.1607	0.1748	0.2142	0.0047	0.0553	-0.0508	-0.0144	-0.0129	0.038	-0.0496	0.0442	0.0082	0.1685	0.048	0.0211	0.2524	-0.0672	0.0647	18.504	-20.5487	42.0824
2	0.8262	-0.1664	0.3315	0.1686	-0.3152	0.6869	0.0562	-0.0762	-0.0387	0.0044	-0.0253	0.0001	-0.0971	-0.0507	-0.0308	0.181	-0.0349	0.0402	0.2392	0.0005	0.0372	55.2553	-22.3915	19.5278
3	0.8858	0.0229	-0.1697	0.216	-0.3326	0.5613	0.0742	-0.0207	-0.0495	0.025	-0.0861	-0.026	-0.0211	0.0534	0.0119	0.1274	-0.0801	-0.0198	0.2579	0.093	0.0766	42.783	-48.6092	62.3101
4	0.7991	-0.0393	0.0495	0.1417	0.1925	0.4892	0.1212	0.0638	-0.0845	-0.0339	-0.1266	0.0876	0.0215	0.0052	0.0054	0.1557	0.0935	-0.0907	0.2532	-0.1692	0.1206	30.7226	-47.5255	-1.0013
5	0.6748	0.39	0.6459	0.9516	0.0953	0.7523	-0.178	0.4329	-0.0305	0.0531	0.2909	0.1114	-0.1654	0.3599	-0.113	0.1201	-0.1178	0.0111	0.4688	-0.0391	0.0431	95.7217	-32.4003	21.429
6	0.4939	0.2947	0.7022	1.1254	-0.0924	1.2897	-0.0748	-0.1086	0.0006	-0.0463	0.1143	0.0098	-0.0689	-0.2266	-0.0396	0.0398	-0.0148	-0.0508	0.2872	0.0576	0.0964	-22.29	-38.2	40.9494

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 506
2	X-RAY DIFFRACTION	2	B	12 - 502
3	X-RAY DIFFRACTION	3	C	12 - 502
4	X-RAY DIFFRACTION	4	D	12 - 502
5	X-RAY DIFFRACTION	5	E	12 - 502
6	X-RAY DIFFRACTION	6	F	13 - 502

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