PDB-2pno: Crystal structure of human leukotriene C4 synthase

ID or keywords:

Entry

Database: PDB / ID: 2pno

Title

Crystal structure of human leukotriene C4 synthase

Components

Leukotriene C4 synthase

Keywords

LYASE / membrane protein / helix bundle / homo trimer / mGST / MAPEG

Function / homology

Function and homology information

Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of 5-eicosatetraenoic acids / Biosynthesis of Lipoxins (LX) / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.3 Å

Authors

Ago, H. / Kanaoka, Y. / Irikura, D. / Lam, B.K. / Shimamura, T. / Austen, K.F. / Miyano, M.

Citation

Journal: Nature / Year: 2007
Title: Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis
Authors: Ago, H. / Kanaoka, Y. / Irikura, D. / Lam, B.K. / Shimamura, T. / Austen, K.F. / Miyano, M.

History

Deposition	Apr 24, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 7, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Dec 7, 2011	Group: Non-polymer description
Revision 1.3	Mar 13, 2024	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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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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PDBx/mmCIF format	2pno.cif.gz	371.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2pno.ent.gz	304.1 KB	Display	PDB format
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Validation report

Summary document	2pno_validation.pdf.gz	10.9 MB	Display	wwPDB validaton report
Full document	2pno_full_validation.pdf.gz	11 MB	Display
Data in XML	2pno_validation.xml.gz	74.3 KB	Display
Data in CIF	2pno_validation.cif.gz	89.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/2pno ftp://data.pdbj.org/pub/pdb/validation_reports/pn/2pno	HTTPS FTP

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Related structure data

Similar structure data	3hkk-1 4ntb-1 4j7t-1 4jcz-1 4nta-1 2uui-1 4ntf-1 2uuh-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Leukotriene C4 synthase

B: Leukotriene C4 synthase

C: Leukotriene C4 synthase

D: Leukotriene C4 synthase

E: Leukotriene C4 synthase

F: Leukotriene C4 synthase

G: Leukotriene C4 synthase

H: Leukotriene C4 synthase

I: Leukotriene C4 synthase

J: Leukotriene C4 synthase

K: Leukotriene C4 synthase

L: Leukotriene C4 synthase

hetero molecules

242 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Leukotriene C4 synthase

B: Leukotriene C4 synthase

C: Leukotriene C4 synthase

hetero molecules

defined by author&software
63.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Leukotriene C4 synthase

E: Leukotriene C4 synthase

F: Leukotriene C4 synthase

hetero molecules

defined by author&software
61.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Leukotriene C4 synthase

H: Leukotriene C4 synthase

I: Leukotriene C4 synthase

hetero molecules

defined by author&software
58.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Leukotriene C4 synthase

K: Leukotriene C4 synthase

L: Leukotriene C4 synthase

hetero molecules

defined by author&software
57.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.500, 293.900, 206.500
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

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	GLU	GLU	PHE	PHE	A	A	4 - 130	4 - 130
2	1	GLU	GLU	PHE	PHE	B	B	4 - 130	4 - 130
3	1	GLU	GLU	PHE	PHE	C	C	4 - 130	4 - 130
4	1	GLU	GLU	PHE	PHE	D	D	4 - 130	4 - 130
5	1	GLU	GLU	PHE	PHE	E	E	4 - 130	4 - 130
6	1	GLU	GLU	PHE	PHE	F	F	4 - 130	4 - 130
7	1	GLU	GLU	PHE	PHE	G	G	4 - 130	4 - 130
8	1	GLU	GLU	PHE	PHE	H	H	4 - 130	4 - 130
9	1	GLU	GLU	PHE	PHE	I	I	4 - 130	4 - 130
10	1	GLU	GLU	PHE	PHE	J	J	4 - 130	4 - 130
11	1	GLU	GLU	PHE	PHE	K	K	4 - 130	4 - 130
12	1	GLU	GLU	PHE	PHE	L	L	4 - 130	4 - 130
1	2	ALA	ALA	LEU	LEU	A	A	133 - 140	133 - 140
2	2	ALA	ALA	LEU	LEU	B	B	133 - 140	133 - 140
3	2	ALA	ALA	LEU	LEU	C	C	133 - 140	133 - 140
4	2	ALA	ALA	LEU	LEU	D	D	133 - 140	133 - 140
5	2	ALA	ALA	LEU	LEU	E	E	133 - 140	133 - 140
6	2	ALA	ALA	LEU	LEU	F	F	133 - 140	133 - 140
7	2	ALA	ALA	LEU	LEU	G	G	133 - 140	133 - 140
8	2	ALA	ALA	LEU	LEU	H	H	133 - 140	133 - 140
9	2	ALA	ALA	LEU	LEU	I	I	133 - 140	133 - 140
10	2	ALA	ALA	LEU	LEU	J	J	133 - 140	133 - 140
11	2	ALA	ALA	LEU	LEU	K	K	133 - 140	133 - 140
12	2	ALA	ALA	LEU	LEU	L	L	133 - 140	133 - 140
1	3	ARG	ARG	LEU	LEU	A	A	142 - 147	142 - 147
2	3	ARG	ARG	LEU	LEU	B	B	142 - 147	142 - 147
3	3	ARG	ARG	LEU	LEU	C	C	142 - 147	142 - 147
4	3	ARG	ARG	LEU	LEU	D	D	142 - 147	142 - 147
5	3	ARG	ARG	LEU	LEU	E	E	142 - 147	142 - 147
6	3	ARG	ARG	LEU	LEU	F	F	142 - 147	142 - 147
7	3	ARG	ARG	LEU	LEU	G	G	142 - 147	142 - 147
8	3	ARG	ARG	LEU	LEU	H	H	142 - 147	142 - 147
9	3	ARG	ARG	LEU	LEU	I	I	142 - 147	142 - 147
10	3	ARG	ARG	LEU	LEU	J	J	142 - 147	142 - 147
11	3	ARG	ARG	LEU	LEU	K	K	142 - 147	142 - 147
12	3	ARG	ARG	LEU	LEU	L	L	142 - 147	142 - 147

NCS ensembles :

ID
1
2
3

#1: Protein	Leukotriene C4 synthase / Leukotriene-C4 / synthase / LTC4 synthase Mass: 17411.539 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pESP-3 / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q16873, leukotriene-C4 synthase
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Sugar	... ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 4.26 Å³/Da / Density % sol: 71.16 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes/NaOH, 30%(v/v) PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SPring-8	BL44B2	1	1
SYNCHROTRON	SPring-8	BL44B2	2	0.97904, 0.97949, 0.96423, 0.99519

Detector

Type	ID	Detector	Date
ADSC QUANTUM 210	1	CCD	Oct 4, 2006
ADSC QUANTUM 210	2	CCD	Nov 13, 2006

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.97904	1
3	0.97949	1
4	0.96423	1
5	0.99519	1

Reflection

Resolution: 3.3→50 Å / Num. obs: 54085 / % possible obs: 99.9 % / Redundancy: 7.5 % / B_iso Wilson estimate: 97.2 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 20.3

Reflection shell

Resolution: 3.3→3.48 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.443 / Mean I/σ(I) obs: 4.3 / Num. unique all: 7797 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
MOSFLM		data reduction
SCALA		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

MAD / Resolution: 3.3→15 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.902 / SU B: 21.07 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25462	2675	5 %	RANDOM
R_work	0.22109	-	-	-
obs	0.22281	50769	99.99 %	-

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 mean: 65.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.1 Å²	0 Å²	0 Å²
2-	-	1.55 Å²	0 Å²
3-	-	-	-1.45 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13353	0	1170	0	14523

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	14935
X-RAY DIFFRACTION	r_angle_refined_deg	0.975	2.048	20206
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.696	5	1760
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.226	20.682	513
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.876	15	1959
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.685	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2412
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	10606
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.1	7884
X-RAY DIFFRACTION	r_nbtor_refined	0.329	0.2	10191
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	459
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.184	0.1	88
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.318	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.659	1.5	8870
X-RAY DIFFRACTION	r_mcangle_it	1.196	2	13810
X-RAY DIFFRACTION	r_scbond_it	1.674	3	6721
X-RAY DIFFRACTION	r_scangle_it	2.907	4.5	6386

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	507	tight positional	0.05	0.05
1	2	B	507	tight positional	0.05	0.05
1	3	C	507	tight positional	0.05	0.05
1	4	D	507	tight positional	0.06	0.05
1	5	E	507	tight positional	0.05	0.05
1	6	F	507	tight positional	0.05	0.05
1	7	G	507	tight positional	0.05	0.05
1	8	H	507	tight positional	0.05	0.05
1	9	I	507	tight positional	0.05	0.05
1	10	J	507	tight positional	0.06	0.05
1	11	K	507	tight positional	0.05	0.05
1	12	L	507	tight positional	0.05	0.05
2	1	A	32	tight positional	0.03	0.05
2	2	B	32	tight positional	0.05	0.05
2	3	C	32	tight positional	0.06	0.05
2	4	D	32	tight positional	0.08	0.05
2	5	E	32	tight positional	0.07	0.05
2	6	F	32	tight positional	0.05	0.05
2	7	G	32	tight positional	0.05	0.05
2	8	H	32	tight positional	0.03	0.05
2	9	I	32	tight positional	0.03	0.05
2	10	J	32	tight positional	0.05	0.05
2	11	K	32	tight positional	0.04	0.05
2	12	L	32	tight positional	0.06	0.05
3	1	A	24	tight positional	0.03	0.05
3	2	B	24	tight positional	0.04	0.05
3	3	C	24	tight positional	0.06	0.05
3	4	D	24	tight positional	0.06	0.05
3	5	E	24	tight positional	0.04	0.05
3	6	F	24	tight positional	0.07	0.05
3	7	G	24	tight positional	0.03	0.05
3	8	H	24	tight positional	0.04	0.05
3	9	I	24	tight positional	0.04	0.05
3	10	J	24	tight positional	0.04	0.05
3	11	K	24	tight positional	0.04	0.05
3	12	L	24	tight positional	0.05	0.05
1	1	A	445	medium positional	0.45	0.5
1	2	B	445	medium positional	0.31	0.5
1	3	C	445	medium positional	0.35	0.5
1	4	D	445	medium positional	0.34	0.5
1	5	E	445	medium positional	0.34	0.5
1	6	F	445	medium positional	0.38	0.5
1	7	G	445	medium positional	0.29	0.5
1	8	H	445	medium positional	0.3	0.5
1	9	I	445	medium positional	0.32	0.5
1	10	J	445	medium positional	0.41	0.5
1	11	K	445	medium positional	0.33	0.5
1	12	L	445	medium positional	0.33	0.5
2	1	A	17	medium positional	0.61	0.5
2	2	B	17	medium positional	0.57	0.5
2	3	C	17	medium positional	1.17	0.5
2	4	D	17	medium positional	0.7	0.5
2	5	E	17	medium positional	0.67	0.5
2	6	F	17	medium positional	0.52	0.5
2	7	G	17	medium positional	0.7	0.5
2	8	H	17	medium positional	0.59	0.5
2	9	I	17	medium positional	0.59	0.5
2	10	J	17	medium positional	0.71	0.5
2	11	K	17	medium positional	0.47	0.5
2	12	L	17	medium positional	0.5	0.5
3	1	A	6	medium positional	0.08	0.5
3	2	B	6	medium positional	0.15	0.5
3	3	C	6	medium positional	0.18	0.5
3	4	D	6	medium positional	0.16	0.5
3	5	E	6	medium positional	0.11	0.5
3	6	F	6	medium positional	0.12	0.5
3	7	G	6	medium positional	0.07	0.5
3	8	H	6	medium positional	0.1	0.5
3	9	I	6	medium positional	0.08	0.5
3	10	J	6	medium positional	0.08	0.5
3	11	K	6	medium positional	0.08	0.5
3	12	L	6	medium positional	0.11	0.5
1	1	A	507	tight thermal	0.12	0.5
1	2	B	507	tight thermal	0.13	0.5
1	3	C	507	tight thermal	0.11	0.5
1	4	D	507	tight thermal	0.11	0.5
1	5	E	507	tight thermal	0.12	0.5
1	6	F	507	tight thermal	0.11	0.5
1	7	G	507	tight thermal	0.08	0.5
1	8	H	507	tight thermal	0.11	0.5
1	9	I	507	tight thermal	0.11	0.5
1	10	J	507	tight thermal	0.16	0.5
1	11	K	507	tight thermal	0.13	0.5
1	12	L	507	tight thermal	0.11	0.5
2	1	A	32	tight thermal	0.06	0.5
2	2	B	32	tight thermal	0.08	0.5
2	3	C	32	tight thermal	0.09	0.5
2	4	D	32	tight thermal	0.1	0.5
2	5	E	32	tight thermal	0.07	0.5
2	6	F	32	tight thermal	0.08	0.5
2	7	G	32	tight thermal	0.06	0.5
2	8	H	32	tight thermal	0.09	0.5
2	9	I	32	tight thermal	0.08	0.5
2	10	J	32	tight thermal	0.09	0.5
2	11	K	32	tight thermal	0.06	0.5
2	12	L	32	tight thermal	0.09	0.5
3	1	A	24	tight thermal	0.06	0.5
3	2	B	24	tight thermal	0.07	0.5
3	3	C	24	tight thermal	0.08	0.5
3	4	D	24	tight thermal	0.04	0.5
3	5	E	24	tight thermal	0.04	0.5
3	6	F	24	tight thermal	0.05	0.5
3	7	G	24	tight thermal	0.06	0.5
3	8	H	24	tight thermal	0.04	0.5
3	9	I	24	tight thermal	0.04	0.5
3	10	J	24	tight thermal	0.04	0.5
3	11	K	24	tight thermal	0.04	0.5
3	12	L	24	tight thermal	0.05	0.5
1	1	A	445	medium thermal	1.11	2
1	2	B	445	medium thermal	1.1	2
1	3	C	445	medium thermal	0.82	2
1	4	D	445	medium thermal	0.78	2
1	5	E	445	medium thermal	0.77	2
1	6	F	445	medium thermal	0.71	2
1	7	G	445	medium thermal	0.56	2
1	8	H	445	medium thermal	0.75	2
1	9	I	445	medium thermal	0.79	2
1	10	J	445	medium thermal	1.1	2
1	11	K	445	medium thermal	1.08	2
1	12	L	445	medium thermal	0.64	2
2	1	A	17	medium thermal	0.35	2
2	2	B	17	medium thermal	0.47	2
2	3	C	17	medium thermal	0.53	2
2	4	D	17	medium thermal	0.58	2
2	5	E	17	medium thermal	0.33	2
2	6	F	17	medium thermal	0.28	2
2	7	G	17	medium thermal	0.47	2
2	8	H	17	medium thermal	0.55	2
2	9	I	17	medium thermal	0.47	2
2	10	J	17	medium thermal	0.42	2
2	11	K	17	medium thermal	0.58	2
2	12	L	17	medium thermal	0.36	2
3	1	A	6	medium thermal	0.11	2
3	2	B	6	medium thermal	0.19	2
3	3	C	6	medium thermal	0.28	2
3	4	D	6	medium thermal	0.27	2
3	5	E	6	medium thermal	0.11	2
3	6	F	6	medium thermal	0.2	2
3	7	G	6	medium thermal	0.25	2
3	8	H	6	medium thermal	0.2	2
3	9	I	6	medium thermal	0.17	2
3	10	J	6	medium thermal	0.14	2
3	11	K	6	medium thermal	0.15	2
3	12	L	6	medium thermal	0.21	2

LS refinement shell

Resolution: 3.3→3.381 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.379	190	-
R_work	0.313	3577	-
obs	-	-	100 %

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Open data

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

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Yorodumi