PDB-4f40: X-ray crystal structure of Apo prostaglandin f synthase from Leis...

ID or keywords:

Entry

Database: PDB / ID: 4f40

Title

X-ray crystal structure of Apo prostaglandin f synthase from Leishmania major Friedlin

Components

Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NADP

Function / homology

Function and homology information

prostaglandin H2 endoperoxidase reductase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / prostaglandin biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP.
Authors: Moen, S.O. / Fairman, J.W. / Barnes, S.R. / Sullivan, A. / Nakazawa-Hewitt, S. / Van Voorhis, W.C. / Staker, B.L. / Lorimer, D.D. / Myler, P.J. / Edwards, T.E.

History

Deposition	May 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2015	Group: Database references
Revision 1.2	Jun 3, 2015	Group: Database references
Revision 1.3	Sep 13, 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 / 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_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	4f40.cif.gz	247 KB	Display	PDBx/mmCIF format
PDB format	pdb4f40.ent.gz	196.5 KB	Display	PDB format
PDBx/mmJSON format	4f40.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4f40_validation.pdf.gz	471.5 KB	Display	wwPDB validaton report
Full document	4f40_full_validation.pdf.gz	473.4 KB	Display
Data in XML	4f40_validation.xml.gz	29 KB	Display
Data in CIF	4f40_validation.cif.gz	45.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/4f40 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f40	HTTPS FTP

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Related structure data

Related structure data	4fziC 4g5dC 4gieC 1vbjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3omm-2 3gg3-d 5nfp-d 1a9t-d 1v48-d 5nft-d 5q0u-2 2a4a-2 6ji6-d 5q1h-4 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
Other databases	TargetTrack: SSGCID-LemaA.00019.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (8)

Deposited unit

A: Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase

B: Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase

hetero molecules

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

1

A: Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase

hetero molecules

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

2

B: Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	94.550, 34.590, 107.200
Angle α, β, γ (deg.)	90.000, 103.220, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase / prostaglandin f synthase Mass: 32187.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: PGFS, LMJF_31_2150 / Production host: Escherichia coli (E. coli) References: UniProt: Q4Q646, UniProt: P22045*PLUS, prostaglandin-F synthase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.65 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate, pH 5.50, 20% PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.977408 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2012

Radiation

Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.977408 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. all: 90336 / Num. obs: 89147 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 19.715 Å² / R_merge(I) obs: 0.083 / Net I/σ(I): 13.33

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.6-1.64		0.578	2.37	21027	5975	90.2
1.64-1.69		0.511	2.97	25609	6376	99.2
1.69-1.74		0.417	3.73	25395	6198	98
1.74-1.79		0.349	4.44	24862	6035	99.8
1.79-1.85		0.303	5.08	24256	5849	98.4
1.85-1.91		0.231	6.58	23566	5717	99.5
1.91-1.98		0.181	8.37	22783	5462	99.3
1.98-2.07		0.148	9.84	21848	5275	99.2
2.07-2.16		0.117	12.13	21200	5128	99.7
2.16-2.26		0.094	14.67	20141	4848	99.6
2.26-2.39		0.087	15.58	19174	4628	99.6
2.39-2.53		0.076	17.33	18177	4407	99.8
2.53-2.7		0.066	19.53	17275	4191	99.7
2.7-2.92		0.055	22.94	15863	3870	99.9
2.92-3.2		0.046	26.17	14497	3563	99.8
3.2-3.58		0.036	31.51	13062	3243	99.6
3.58-4.13		0.031	35.07	11466	2883	99.8
4.13-5.06		0.028	37.57	9854	2463	99.4
5.06-7.16		0.031	31.25	7790	1929	99.8
	7.16	0.022	34.43	4206	1107	98.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	dev_1048	refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VBJ

1vbj

Resolution: 1.6→46.19 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.9052 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 16.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1802	4466	5.01 %	RANDOM
R_work	0.1538	-	-	-
obs	0.1551	89114	98.69 %	-
all	-	90336	-	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 57.84 Å² / B_iso mean: 15.0583 Å² / B_iso min: 2.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→46.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4366	0	99	674	5139

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4602
X-RAY DIFFRACTION	f_angle_d	1.54	6237
X-RAY DIFFRACTION	f_chiral_restr	0.11	689
X-RAY DIFFRACTION	f_plane_restr	0.008	805
X-RAY DIFFRACTION	f_dihedral_angle_d	13.661	1677

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6182	0.2228	135	0.2151	2444	2579	87
1.6182-1.6372	0.2691	131	0.2113	2653	2784	92
1.6372-1.6572	0.253	162	0.1995	2761	2923	97
1.6572-1.6781	0.2449	159	0.1973	2779	2938	100
1.6781-1.7002	0.1842	155	0.1868	2800	2955	99
1.7002-1.7235	0.2546	127	0.1716	2839	2966	98
1.7235-1.7481	0.2216	150	0.1759	2755	2905	99
1.7481-1.7742	0.2029	154	0.1734	2795	2949	100
1.7742-1.802	0.2318	166	0.1672	2826	2992	99
1.802-1.8315	0.1789	133	0.164	2786	2919	98
1.8315-1.8631	0.1905	143	0.1559	2812	2955	100
1.8631-1.897	0.1791	148	0.1518	2829	2977	100
1.897-1.9334	0.1851	137	0.1502	2833	2970	98
1.9334-1.9729	0.1666	138	0.1508	2823	2961	100
1.9729-2.0158	0.1826	157	0.1522	2849	3006	100
2.0158-2.0627	0.1621	137	0.1498	2817	2954	99
2.0627-2.1143	0.1633	145	0.1427	2829	2974	100
2.1143-2.1714	0.1827	159	0.1405	2841	3000	99
2.1714-2.2353	0.1565	162	0.1396	2810	2972	100
2.2353-2.3075	0.1715	155	0.1421	2870	3025	100
2.3075-2.39	0.1744	155	0.1427	2812	2967	100
2.39-2.4856	0.1752	148	0.1453	2877	3025	100
2.4856-2.5988	0.1789	137	0.1473	2852	2989	100
2.5988-2.7358	0.1731	159	0.1508	2849	3008	100
2.7358-2.9071	0.1807	152	0.1487	2894	3046	100
2.9071-3.1316	0.1522	142	0.1578	2900	3042	100
3.1316-3.4466	0.1676	162	0.1519	2888	3050	100
3.4466-3.9451	0.1525	132	0.1419	2898	3030	100
3.9451-4.9695	0.1527	155	0.1337	2933	3088	100
4.9695-46.2089	0.2253	171	0.1733	2994	3165	99

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	2.6682	-1.4934	-0.5464	1.2367	0.6592	1.4605	0.0136	0.0951	-0.052	0.1037	-0.0026	0.1516	-0.0873	-0.1164	0.0049	0.0869	-0.0014	0.0244	0.0694	0.0273	0.088	35.819	0.1518	19.6617
2	1.1925	-0.2202	0.0963	1.025	0.0067	0.7102	-0.0133	-0.1544	-0.0178	0.204	0.0213	0.0549	0.0125	-0.0159	-0.0056	0.0797	0.006	0.0079	0.0476	0.0043	0.0408	45.7817	5.3116	23.6513
3	2.5499	-0.3663	0.4119	1.4136	0.0859	1.7825	0.0015	0.0702	0.2028	0.0604	-0.0111	0.2349	-0.184	-0.1993	0.0028	0.0758	0.0165	0.0202	0.0714	0.0093	0.1027	41.9483	4.6899	8.275
4	1.7307	-0.3679	0.3026	1.385	0.1719	1.0555	-0.003	0.3164	0.1064	-0.0255	0.0476	0.278	0.0716	-0.3976	-0.0175	0.0573	-0.0072	0.0096	0.211	0.0421	0.1368	26.579	5.5495	8.6554
5	1.2058	-0.1448	0.0058	0.3529	-0.3193	1.3481	-0.0801	0.1187	-0.039	-0.0365	0.0686	0.0962	0.0899	-0.2286	0.0169	0.0713	0.0008	0.0079	0.0952	-0.0069	0.0781	35.4402	8.7211	5.1299
6	2.7026	1.3931	-0.8793	1.9711	-1.2634	1.7533	-0.0493	0.0581	-0.0852	-0.1483	-0.0093	-0.2448	-0.0099	0.1795	0.0488	0.0866	0.0011	0.0256	0.0799	-0.0299	0.0741	1.0097	2.305	28.7732
7	1.1959	0.2039	0.1688	1.1029	-0.0604	0.7999	0.0103	0.1084	-0.0119	-0.1904	0.0172	0.0406	0.0092	-0.0187	-0.0179	0.0685	-0.0022	-0.0185	0.0377	-0.001	0.047	-13.9203	5.6014	29.1332
8	2.3128	0.2104	0.4637	1.4228	0.0172	1.9374	0.0147	-0.0527	0.2384	-0.0012	-0.004	-0.1877	-0.1753	0.1872	-0.0211	0.0746	-0.0135	0.0103	0.0688	-0.0138	0.0997	-6.7905	5.3293	43.9013
9	1.5899	0.1792	0.2224	1.2745	-0.2174	0.9998	0.0232	-0.2618	0.1333	-0.0157	0.0604	-0.2571	0.0786	0.4486	-0.034	0.0465	0.0008	0.014	0.2058	-0.0468	0.1376	7.7589	5.5959	41.7945
10	1.2223	0.1947	0.036	0.5443	0.3793	1.3484	-0.0722	-0.1432	-0.0467	0.0443	0.1032	-0.0934	0.0756	0.2377	-0.0267	0.0583	0.0021	0.0043	0.1032	-0.0084	0.0744	-0.6445	8.7822	46.5092

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 3:30)	A	3 - 30
2	X-RAY DIFFRACTION	2	(chain A and resid 31:181)	A	31 - 181
3	X-RAY DIFFRACTION	3	(chain A and resid 182:207)	A	182 - 207
4	X-RAY DIFFRACTION	4	(chain A and resid 208:248)	A	208 - 248
5	X-RAY DIFFRACTION	5	(chain A and resid 249:284)	A	249 - 284
6	X-RAY DIFFRACTION	6	(chain B and resid 3:43)	B	3 - 43
7	X-RAY DIFFRACTION	7	(chain B and resid 44:181)	B	44 - 181
8	X-RAY DIFFRACTION	8	(chain B and resid 182:208)	B	182 - 208
9	X-RAY DIFFRACTION	9	(chain B and resid 209:248)	B	209 - 248
10	X-RAY DIFFRACTION	10	(chain B and resid 249:284)	B	249 - 284

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