PDB-7uor: Crystal structure of cytochrome P450 enzyme CYP119 in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 7uor

Title

Crystal structure of cytochrome P450 enzyme CYP119 in complex with methyliridium(III) mesoporphyrin.

Components

Cytochrome

Keywords

OXIDOREDUCTASE / Cytochrome P450 Iridium

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

Sulfolobus acidocaldarius (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.16 Å

Authors

Pereira, J.H. / Bloomer, B.J. / Hartwig, J.F. / Adams, P.D.

Funding support

United States, 1items

Citation

Journal: Nat Catal / Year: 2023
Title: Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics
Authors: Bloomer, B.J. / Natoli, S.N. / Garcia-Borras, M. / Pereira, J.H. / Hu, D.B. / Adams, P.D. / Houk, K.N. / Clark, D.S. / Hartwig, J.F.

History

Deposition	Apr 13, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7uor.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7uor.ent.gz	804.9 KB	Display	PDB format
PDBx/mmJSON format	7uor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7uor_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	7uor_full_validation.pdf.gz	2.6 MB	Display
Data in XML	7uor_validation.xml.gz	89.3 KB	Display
Data in CIF	7uor_validation.cif.gz	116.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uo/7uor ftp://data.pdbj.org/pub/pdb/validation_reports/uo/7uor	HTTPS FTP

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Related structure data

Related structure data	5bv5S S: Starting model for refinement
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 (1)

Deposited unit

A: Cytochrome

B: Cytochrome

C: Cytochrome

D: Cytochrome

E: Cytochrome

F: Cytochrome

hetero molecules

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

1

A: Cytochrome

hetero molecules

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

2

B: Cytochrome

hetero molecules

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

3

C: Cytochrome

hetero molecules

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

4

D: Cytochrome

hetero molecules

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

5

E: Cytochrome

hetero molecules

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

6

F: Cytochrome

hetero molecules

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

Unit cell

Length a, b, c (Å)	190.213, 190.213, 266.773
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4
Space group name Hall	I4
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: -y+1/2,x+1/2,z+1/2 #7: y+1/2,-x+1/2,z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	chain "B"
d_3	ens_1	chain "C"
d_4	ens_1	chain "D"
d_5	ens_1	chain "E"
d_6	ens_1	chain "F"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	HIS	ASN	A	1 - 379
d_1	2	ens_1	HIR	HIR	B
d_1	3	ens_1	BTB	BTB	C
d_2	1	ens_1	HIS	ASN	D	1 - 379
d_2	2	ens_1	HIR	HIR	E
d_2	3	ens_1	BTB	BTB	F
d_3	1	ens_1	HIS	ASN	G	1 - 379
d_3	2	ens_1	HIR	HIR	H
d_3	3	ens_1	BTB	BTB	I
d_4	1	ens_1	HIS	ASN	J	1 - 379
d_4	2	ens_1	HIR	HIR	K
d_4	3	ens_1	BTB	BTB	L
d_5	1	ens_1	HIS	ASN	M	1 - 379
d_5	2	ens_1	HIR	HIR	N
d_5	3	ens_1	BTB	BTB	O
d_6	1	ens_1	HIS	ASN	P	1 - 379
d_6	2	ens_1	HIR	HIR	Q
d_6	3	ens_1	BTB	BTB	R

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.514049514978, -0.57558760388, 0.635965412905), (0.382472069799, 0.509828729497, 0.770577564171), (-0.76776833223, 0.639354030909, -0.0419310289132)	-27.0297376666, -32.6997663471, 44.6899301911
2	given	(-0.487282678765, 0.40326990578, -0.774550820842), (-0.584486343032, 0.508378926632, 0.63239748716), (0.648792189984, 0.760870718354, -0.0120184927128)	34.0308011882, -27.1897510973, 44.0474619193
3	given	(0.487698656087, 0.602876808931, 0.63141869952), (-0.409925296778, -0.480432500062, 0.775335968433), (0.770786138895, -0.636964807613, 0.0128281702013)	67.4433534123, -129.019423939, -88.811669536
4	given	(-0.186973904217, 0.982118432919, -0.0220032466445), (0.982202304753, 0.187303539091, 0.014000599377), (0.0178715326881, -0.0189938928394, -0.99965986233)	95.1616191024, -95.485046792, -45.5619489099
5	given	(-0.490659644342, 0.41998322611, 0.763457401038), (-0.578603865975, 0.498083013743, -0.645856700592), (-0.651514143893, -0.758635222756, -0.001385316104)	61.6729737843, -67.062313653, -87.8846624437

#1: Protein	Cytochrome Mass: 45049.219 Da / Num. of mol.: 6 / Mutation: L155W, T213G, V254L, C317G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: ATY89_07675, ATZ20_10695 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3HD14
#2: Chemical	ChemComp-HIR / methyliridium(III) mesoporphyrin Mass: 780.869 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₅H₃₂IrN₄O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#4: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
Has ligand of interest	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: 4.46 Å³/Da / Density % sol: 72.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate 0.1 M Bis-TRIS pH 6.5 25 % Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.159→60.15 Å / Num. obs: 80832 / % possible obs: 99.88 % / Redundancy: 9.2 % / B_iso Wilson estimate: 83.69 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.2178 / Net I/σ(I): 7.86
Reflection shell	Resolution: 3.159→3.272 Å / Num. unique obs: 8034 / CC_1/2: 0.406

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4444	refinement
PHENIX	1.20_4444	refinement
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5BV5

5bv5

Resolution: 3.16→60.15 Å / SU ML: 0.4495 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2294	4000	4.95 %
R_work	0.181	76764	-
obs	0.1834	80764	99.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 88.88 Å²

Refinement step

Cycle: LAST / Resolution: 3.16→60.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18798	0	356	0	19154

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0116	19626
X-RAY DIFFRACTION	f_angle_d	1.7522	26622
X-RAY DIFFRACTION	f_chiral_restr	0.091	2820
X-RAY DIFFRACTION	f_plane_restr	0.0126	3390
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0854	7416

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.680420182644
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.620378791099
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.664435126684
ens_1	d_5	A	X-RAY DIFFRACTION	Torsion NCS	0.595334763546
ens_1	d_6	A	X-RAY DIFFRACTION	Torsion NCS	0.646288782579

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 (%)
3.16-3.2	0.3915	195	0.3483	2548	X-RAY DIFFRACTION	99.13
3.2-3.24	0.3478	109	0.3304	2625	X-RAY DIFFRACTION	99.93
3.24-3.28	0.2971	142	0.2973	2664	X-RAY DIFFRACTION	100
3.28-3.32	0.3628	151	0.2819	2643	X-RAY DIFFRACTION	100
3.32-3.36	0.3253	138	0.2628	2612	X-RAY DIFFRACTION	99.89
3.36-3.41	0.3105	122	0.2548	2655	X-RAY DIFFRACTION	99.93
3.41-3.46	0.2768	90	0.246	2724	X-RAY DIFFRACTION	99.96
3.46-3.52	0.2988	128	0.2383	2660	X-RAY DIFFRACTION	99.89
3.52-3.58	0.3091	147	0.245	2634	X-RAY DIFFRACTION	99.93
3.58-3.64	0.3095	165	0.2509	2594	X-RAY DIFFRACTION	99.93
3.64-3.7	0.3194	153	0.2576	2636	X-RAY DIFFRACTION	99.93
3.7-3.77	0.271	131	0.2367	2655	X-RAY DIFFRACTION	100
3.77-3.85	0.2492	119	0.1864	2650	X-RAY DIFFRACTION	99.96
3.85-3.94	0.2229	135	0.1787	2656	X-RAY DIFFRACTION	99.96
3.94-4.03	0.2325	116	0.1777	2657	X-RAY DIFFRACTION	99.93
4.03-4.13	0.2204	136	0.1578	2653	X-RAY DIFFRACTION	99.96
4.13-4.24	0.2088	99	0.1675	2662	X-RAY DIFFRACTION	100
4.24-4.36	0.203	161	0.1492	2635	X-RAY DIFFRACTION	99.96
4.36-4.5	0.2063	153	0.1435	2646	X-RAY DIFFRACTION	100
4.5-4.67	0.1856	174	0.1403	2606	X-RAY DIFFRACTION	100
4.67-4.85	0.1851	124	0.1359	2689	X-RAY DIFFRACTION	100
4.85-5.07	0.1896	131	0.1355	2638	X-RAY DIFFRACTION	100
5.07-5.34	0.1837	164	0.1436	2621	X-RAY DIFFRACTION	100
5.34-5.67	0.185	144	0.1665	2663	X-RAY DIFFRACTION	100
5.67-6.11	0.2254	171	0.1652	2645	X-RAY DIFFRACTION	100
6.11-6.73	0.2244	134	0.1778	2643	X-RAY DIFFRACTION	100
6.73-7.7	0.2287	99	0.1672	2701	X-RAY DIFFRACTION	100
7.7-9.69	0.1952	98	0.1337	2717	X-RAY DIFFRACTION	99.96
9.71-60.15	0.1843	171	0.1604	2632	X-RAY DIFFRACTION	98.59

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	1.12612082093	-0.795836685833	-0.391738071994	1.09313229059	0.648824938497	0.814154808291	-0.131537920143	-0.102825669557	-0.0884877337955	0.063374109414	0.0893442335972	0.00172415735872	-0.0045536056306	0.14694039998	-0.00598191771735	0.222833222211	0.000878189657539	0.0515944757271	0.312436598187	-0.0534314824556	0.311040885865	29.3143886253	-51.6984437982	5.05860440474
2	1.01968621543	-0.159821946014	0.363717816869	0.348067667949	0.50646900148	1.18697146212	0.104892062569	0.139693874771	-0.0818781244339	-0.0530001329638	0.0336704936937	0.0601836870242	-0.171101559743	0.0813695051252	0.00998948169155	0.288949938252	0.0471679608966	-0.0899505389863	0.380203092993	-0.0871412045056	0.302055288711	-9.12868293211	-43.9477535105	-11.0850949898
3	0.7179652336	0.361455438649	0.140437780645	1.44896538402	-0.408182023283	0.637304731279	-0.189321732596	-0.120630848713	-0.132811001154	0.0993430605515	0.26341191438	0.46829498715	-0.0358379374734	0.119429099923	0.0297385497866	0.2442834287	-0.0616756308229	-0.0288254721129	0.0721368243846	0.0273450763557	0.45559754585	-5.0211053715	-67.4106747716	23.6691888262
4	0.854768417513	-0.164607172246	-0.367505439933	0.714233813444	-0.410463409856	1.31182595242	0.0335706716926	-0.140489670855	-0.144144484767	0.048577816597	0.0574170322432	-0.15335273877	-0.231246352873	-0.0180122158541	0.00642358144831	0.445672177239	-0.0271785410936	0.087971022922	0.349894500827	0.0754221247522	0.267152836826	53.7656607354	-112.278398012	-33.2176737905
5	0.622994889062	-0.376287238115	-0.766110153207	0.939153063576	1.25302363867	0.700689510974	0.0716092505227	0.140126379634	-0.0750236026989	0.369773894147	-1.0186225156	-0.530273593854	-0.58816506103	0.678393429246	-0.258767693165	0.158673249017	0.357876691374	0.238562857748	-0.0504270404635	-0.699273546098	0.00940090895708	38.795274353	-76.3025249139	-49.1117034872
6	1.70400889717	-0.369303025301	0.603510611447	1.24728535997	0.0293461833265	0.888019058372	0.192432917461	-0.137195438748	0.0157092889801	-0.0477115022751	-0.0795652453952	-0.107652786128	0.40657339241	-0.356049761627	0.0637408435133	0.513088328372	-0.209729612595	0.0203630722018	0.526388437193	-0.0307605961298	0.231265543837	29.4350384778	-113.040264755	-67.7707334741

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: -11 - 367 / Label seq-ID: 1 - 379

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID
1	1	(chain 'A' and ( resid -11:390 ) )	A	A
2	2	(chain 'B' and ( resid -11:390 ) )	B	D
3	3	(chain 'C' and ( resid -11:390 ) )	C	G
4	4	(chain 'D' and ( resid -11:390 ) )	D	J
5	5	(chain 'E' and ( resid -11:390 ) )	E	M
6	6	(chain 'F' and ( resid -11:390 ) )	F	P

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