PDB-4lht: Crystal Structure of P450cin Y81F mutant, crystallized in 3 mM 1,...

ID or keywords:

Entry

Database: PDB / ID: 4lht

Title

Crystal Structure of P450cin Y81F mutant, crystallized in 3 mM 1,8-cineole

Components

P450cin

Keywords

OXIDOREDUCTASE / P450 monooxygenase / cindoxin

Function / homology

Function and homology information

1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding
Similarity search - Function

Biological species

Citrobacter braakii (bacteria)

Method

X-RAY DIFFRACTION /

FOURIER SYNTHESIS / Resolution: 2.137 Å

Authors

Madrona, Y. / Poulos, T.L.

Citation

Journal: Biochemistry / Year: 2013
Title: P450cin active site water: implications for substrate binding and solvent accessibility.
Authors: Madrona, Y. / Hollingsworth, S.A. / Khan, B. / Poulos, T.L.

History

Deposition	Jul 1, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lht.cif.gz	322.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4lht.ent.gz	262.2 KB	Display	PDB format
PDBx/mmJSON format	4lht.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4lht_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4lht_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4lht_validation.xml.gz	35.5 KB	Display
Data in CIF	4lht_validation.cif.gz	50.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lh/4lht ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lht	HTTPS FTP

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Related structure data

Related structure data	4l6gSC 4l77C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4fmx-2 4l77-2 1t2b-2 4l77-1 6oom-d 3be0-2 4fyz-1 2pax-d 5kpq-1 7kk6-1 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

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Links

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

Deposited unit

A: P450cin

B: P450cin

hetero molecules

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

1

A: P450cin

hetero molecules

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

2

B: P450cin

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.460, 103.709, 127.590
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	P450cin Mass: 44771.879 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404 / Mutation: Y81F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pcWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 5-alpha References: UniProt: Q8VQF6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

#1: Protein

P450cin

Mass: 44771.879 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404 / Mutation: Y81F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pcWori-P450cin / Production host:

Escherichia coli (E. coli) / Strain (production host): NEB 5-alpha
References: UniProt: Q8VQF6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 8 types, 432 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-CNL / 1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE / 1,8-CINEOLE Mass: 154.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₈O
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.53 Å³/Da / Density % sol: 51.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 12-15% PEG3350, 100 mM Bis-Tris, pH 6.2, 150 mM lithium sulfate, 3 mM 1,8-cineole, 3 mM TCEP, 100 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 70 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 2, 2012
Radiation	Monochromator: Cu Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.137→50 Å / Num. all: 51079 / Num. obs: 50211 / % possible obs: 95.5 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 27.3 Å² / R_sym value: 0.081 / Net I/σ(I): 19.7
Reflection shell	Highest resolution: 2.137 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.22 / Num. unique all: 4797 / R_sym value: 0.257 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
FFT		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB ENTRY 4L6G

4l6g

Resolution: 2.137→32.884 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.26 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.263	2553	5.09 %	RANDOM
R_work	0.2095	-	-	-
obs	0.2122	50111	98.22 %	-
all	-	51079	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.137→32.884 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6276	0	144	423	6843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6607
X-RAY DIFFRACTION	f_angle_d	1.342	9010
X-RAY DIFFRACTION	f_dihedral_angle_d	15.209	2415
X-RAY DIFFRACTION	f_chiral_restr	0.086	972
X-RAY DIFFRACTION	f_plane_restr	0.006	1158

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.137-2.1783	0.3101	123	0.2331	2457	X-RAY DIFFRACTION	93
2.1783-2.2228	0.2794	134	0.2186	2671	X-RAY DIFFRACTION	100
2.2228-2.2711	0.2638	141	0.1979	2633	X-RAY DIFFRACTION	100
2.2711-2.3239	0.2897	146	0.1997	2653	X-RAY DIFFRACTION	100
2.3239-2.382	0.3085	148	0.199	2639	X-RAY DIFFRACTION	100
2.382-2.4464	0.2733	151	0.1984	2637	X-RAY DIFFRACTION	100
2.4464-2.5183	0.2825	145	0.1937	2658	X-RAY DIFFRACTION	100
2.5183-2.5996	0.2591	133	0.1874	2668	X-RAY DIFFRACTION	100
2.5996-2.6925	0.255	121	0.1884	2661	X-RAY DIFFRACTION	99
2.6925-2.8002	0.2826	150	0.1956	2648	X-RAY DIFFRACTION	99
2.8002-2.9276	0.2823	139	0.2004	2664	X-RAY DIFFRACTION	99
2.9276-3.0818	0.2533	156	0.2019	2649	X-RAY DIFFRACTION	99
3.0818-3.2748	0.2367	161	0.2095	2659	X-RAY DIFFRACTION	99
3.2748-3.5273	0.2483	145	0.2135	2656	X-RAY DIFFRACTION	99
3.5273-3.8818	0.2643	129	0.2133	2644	X-RAY DIFFRACTION	97
3.8818-4.4423	0.2324	124	0.2083	2569	X-RAY DIFFRACTION	94
4.4423-5.5924	0.2348	159	0.2134	2589	X-RAY DIFFRACTION	94
5.5924-32.8881	0.3013	148	0.2489	2803	X-RAY DIFFRACTION	97

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	0.1842	0.1099	-0.1816	0.1123	-0.0475	0.1071	0.0401	-0.0099	-0.1348	-0.0386	-0.0218	-0.0481	-0.2061	0.1251	-0.0005	0.1459	-0.0018	0.0104	0.1529	0.0064	0.1212	13.9416	19.8789	38.7927
2	0.0549	-0.0551	0.1011	0.1329	0.1241	0.172	-0.1015	-0.1891	0.1379	0.1238	0.1385	-0.1229	-0.0172	0.0711	0.0037	0.1332	-0.0176	-0.0178	0.2974	-0.0165	0.3139	26.0015	12.6102	41.9057
3	1.0765	0.0265	-0.2981	0.2714	-0.0925	0.3124	0.4975	-0.0888	0.0363	0.2833	-0.3748	0.2367	0.244	0.5143	0.1704	0.2088	0.1888	-0.1288	0.1717	0.0406	0.085	26.7054	2.5848	19.266
4	0.3329	-0.2749	0.5329	0.3867	0.0422	0.4702	0.0058	-0.1138	-0.2165	-0.0791	-0.1149	0.2594	0.2416	-0.0374	-0.0839	0.226	0.0846	-0.041	0.2369	0.0122	0.1844	25.9984	-3.9033	34.7428
5	0.6839	0.6544	0.6561	1.6855	1.0547	1.4229	0.0369	-0.0033	0.3338	0.0555	-0.6316	0.0137	0.3537	0.5891	-0.534	0.1494	0.0536	-0.0051	0.3474	0.2035	0.1857	38.915	7.8679	36.0363
6	0.463	-0.0523	0.0699	0.2118	0.1719	0.141	0.0961	0.0441	-0.0891	0.0289	-0.0139	0.0716	0.1903	0.0869	0.1714	0.1284	0.0173	-0.0494	0.1325	0.0148	0.129	11.6794	7.0015	19.3106
7	0.4204	0.2665	0.0346	0.0585	-0.0036	0.2555	-0.0254	0.0264	0.0742	0.0165	0.0513	0.0416	-0.0355	0.045	0.0045	0.1402	0.0178	-0.0227	0.0989	0.0206	0.1528	9.3206	19.127	29.5445
8	0.6502	-0.6942	0.3434	0.1797	-0.1059	0.4826	0.1842	0.1225	0.012	0.0212	-0.0292	0.024	0.2418	0.04	0.1778	0.2421	0.0655	-0.0801	0.1684	-0.052	0.1552	13.5812	-3.8133	16.9072
9	0.2732	-0.0235	0.0782	0.229	-0.296	0.3856	-0.0614	0.0646	0.0035	0.0395	0.0504	0.0447	-0.028	0.1359	0.0002	0.1133	0.0101	-0.0101	0.1494	0.0042	0.1657	63.9523	14.1304	-11.2951
10	0.199	0.0556	-0.0604	0.0664	-0.0938	0.2784	-0.1634	0.1061	-0.1851	-0.0824	-0.0164	0.205	0.1248	-0.0674	-0.0645	0.1348	0.0298	-0.0607	0.2646	-0.0155	0.1401	42.4987	12.7951	-16.1889
11	0.2885	0.2538	0.176	-0.0076	-0.5951	0.3657	0.1546	-0.1797	-0.0698	0.1156	-0.0329	0.1643	0.0317	-0.2208	0.0107	0.3677	-0.0116	-0.0457	0.2035	0.0001	0.2789	41.6513	2.7932	6.4678
12	0.3543	0.1472	0.5128	0.3087	-0.1342	0.3908	0.0257	0.003	-0.1548	0.1675	-0.1061	-0.1418	0.0282	0.0434	-0.1697	0.1666	-0.0397	-0.0561	0.1553	-0.0185	0.1734	42.3948	-3.7447	-9.0146
13	0.0666	0.0698	0.0165	0.0986	0.1122	0.0724	-0.0368	-0.1956	0.3014	-0.0055	-0.0276	0.1716	0.133	-0.1667	-0	0.2513	-0.0304	0.0043	0.2392	-0.0699	0.2568	29.547	8.118	-10.3628
14	0.1737	-0.0448	0.1579	0.0452	-0.422	0.1513	0.0262	-0.0509	0.1019	-0.1379	-0.0523	-0.0581	0.1048	-0.0548	-0.0182	0.1284	-0.0003	-0.0472	0.1016	0.0033	0.1336	56.7367	7.1183	6.4691
15	0.4145	0.0803	0.1641	0.343	-0.2451	0.2256	-0.0483	-0.0434	0.1038	0.0672	0.0311	-0.0327	-0.1342	0.0412	-0	0.1629	0.0017	-0.0405	0.1372	-0.0174	0.1825	59.1688	19.1852	-3.7352
16	0.257	0.3548	0.2392	0.1067	-0.0117	0.2861	0.0099	-0.0157	-0.0647	-0.0274	-0.058	-0.0529	0.1688	-0.1575	-0.0275	0.1516	0.0074	-0.0596	0.1369	0.009	0.1515	54.6002	-3.8301	8.9693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and resid 57:80	A	57 - 80
2	X-RAY DIFFRACTION	2	chain A and resid 81:98	A	81 - 98
3	X-RAY DIFFRACTION	3	chain A and resid 99:143	A	99 - 143
4	X-RAY DIFFRACTION	4	chain A and resid 144:197	A	144 - 197
5	X-RAY DIFFRACTION	5	chain A and resid 198:236	A	198 - 236
6	X-RAY DIFFRACTION	6	chain A and resid 237:292	A	237 - 292
7	X-RAY DIFFRACTION	7	chain A and resid 293:351	A	293 - 351
8	X-RAY DIFFRACTION	8	chain A and resid 352:402	A	352 - 402
9	X-RAY DIFFRACTION	9	chain B and resid 8:80	B	8 - 80
10	X-RAY DIFFRACTION	10	chain B and resid 81:98	B	81 - 98
11	X-RAY DIFFRACTION	11	chain B and resid 99:143	B	99 - 143
12	X-RAY DIFFRACTION	12	chain B and resid 144:197	B	144 - 197
13	X-RAY DIFFRACTION	13	chain B and resid 198:236	B	198 - 236
14	X-RAY DIFFRACTION	14	chain B and resid 237:292	B	237 - 292
15	X-RAY DIFFRACTION	15	chain B and resid 293:351	B	293 - 351
16	X-RAY DIFFRACTION	16	chain B and resid 352:403	B	352 - 403

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