PDB-4g5d: X-ray crystal structure of Prostaglandin f synthase from Leishman...

ID or keywords:

Entry

Database: PDB / ID: 4g5d

Title

X-ray crystal structure of Prostaglandin f synthase from Leishmania major Friedlin bound to NADPH

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

Function / homology

Function and homology information

: / 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 /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 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	Jul 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 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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PDBx/mmCIF format	4g5d.cif.gz	250.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4g5d_validation.pdf.gz	973.4 KB	Display	wwPDB validaton report
Full document	4g5d_full_validation.pdf.gz	976.7 KB	Display
Data in XML	4g5d_validation.xml.gz	31.1 KB	Display
Data in CIF	4g5d_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g5/4g5d ftp://data.pdbj.org/pub/pdb/validation_reports/g5/4g5d	HTTPS FTP

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Related structure data

Related structure data	4f40SC 4fziC 4gieC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4otk-d 1vbj-2 1gom-d 1vbj-1 3d3f-2 2wzm-1 2bnj-d 3f7j-1 1m9h-d 4oez-d 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) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

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
32.9 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)	94.660, 34.590, 106.950
Angle α, β, γ (deg.)	90.000, 102.980, 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 860 / 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: 53.59 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: JCSG+ B8: 10% PEG8000, 200 mM magnesium chloride, 100 mM Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 5, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 63649 / Num. obs: 61422 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 17.594 Å² / R_merge(I) obs: 0.096 / Net I/σ(I): 13.36

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
1.8-1.85		0.515	2.62	13271	4020	86.7
1.85-1.9		0.424	3.1	13517	4035	88.4
1.9-1.95		0.357	3.66	13531	3953	90.2
1.95-2.01		0.28	4.49	13990	4027	93.1
2.01-2.08		0.24	5.4	13954	3982	96.4
2.08-2.15		0.194	7.07	14828	3973	97.7
2.15-2.23		0.165	9.55	17027	3825	99.1
2.23-2.32		0.158	10.55	17799	3741	98.8
2.32-2.43		0.149	11.08	18071	3601	99.8
2.43-2.55		0.136	12.22	18131	3419	99.4
2.55-2.68		0.13	13.25	18601	3284	99.9
2.68-2.85		0.114	15.59	20055	3100	99.9
2.85-3.04		0.094	19.21	21746	2955	99.9
3.04-3.29		0.08	21.35	19955	2723	99.9
3.29-3.6		0.061	28.57	18464	2526	100
3.6-4.02		0.053	35.15	16622	2296	99.9
4.02-4.65		0.043	40.14	14677	2046	100
4.65-5.69		0.052	30.96	12623	1752	99.7
5.69-8.05		0.064	24.66	9786	1365	99.9
	8.05	0.036	35.51	5193	799	98.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F40

4f40

Resolution: 1.8→46.189 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8788 / SU ML: 0.18 / σ(F): 1.36 / Phase error: 19.54 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2176	3097	5.04 %	RANDOM
R_work	0.1721	-	-	-
obs	0.1744	61405	96.49 %	-
all	-	63649	-	-

Solvent computation

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

Displacement parameters

B_iso max: 56.15 Å² / B_iso mean: 14.454 Å² / B_iso min: 2.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.189 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4402	0	96	860	5358

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4645
X-RAY DIFFRACTION	f_angle_d	1.332	6344
X-RAY DIFFRACTION	f_chiral_restr	0.083	703
X-RAY DIFFRACTION	f_plane_restr	0.006	809
X-RAY DIFFRACTION	f_dihedral_angle_d	16.616	1698

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8282	0.289	131	0.2219	2307	2438	85
1.8282-1.8581	0.2246	131	0.2107	2390	2521	89
1.8581-1.8902	0.2676	120	0.1893	2413	2533	89
1.8902-1.9245	0.2323	144	0.1959	2391	2535	88
1.9245-1.9616	0.2712	129	0.1884	2498	2627	93
1.9616-2.0016	0.2623	107	0.1851	2559	2666	93
2.0016-2.0451	0.2153	153	0.17	2573	2726	94
2.0451-2.0927	0.1872	139	0.1707	2654	2793	98
2.0927-2.145	0.2143	152	0.1674	2682	2834	98
2.145-2.203	0.2266	138	0.1636	2672	2810	98
2.203-2.2679	0.2205	151	0.1686	2699	2850	100
2.2679-2.3411	0.2037	133	0.1694	2723	2856	99
2.3411-2.4247	0.2633	130	0.1713	2750	2880	100
2.4247-2.5218	0.2236	143	0.1745	2721	2864	99
2.5218-2.6366	0.2359	153	0.1736	2734	2887	100
2.6366-2.7755	0.2374	150	0.1715	2725	2875	100
2.7755-2.9494	0.2201	137	0.1726	2766	2903	100
2.9494-3.1771	0.2222	143	0.1735	2781	2924	100
3.1771-3.4967	0.2212	150	0.1607	2778	2928	100
3.4967-4.0024	0.1816	154	0.1587	2762	2916	100
4.0024-5.0417	0.1809	148	0.152	2823	2971	100
5.0417-46.2041	0.193	161	0.1888	2907	3068	100

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	1.5846	-0.5451	-0.3302	1.0314	0.366	1.1098	-0.0654	0.0085	-0.1196	0.1095	0.014	0.2767	0.0223	-0.0959	0.0572	0.0627	0.0014	0.0034	0.0733	0.0097	0.0838	34.8503	1.4954	20.3713
2	2.7127	0.5282	-0.3994	0.4525	-0.5463	0.6902	0.0596	-0.2739	0.0622	0.1988	-0.0922	0.1406	-0.0639	-0.1854	0.0041	0.0789	0.0148	0.0526	0.1063	-0.0042	0.1201	31.8915	6.7069	27.0163
3	1.077	-0.1021	0.2409	0.9842	0.0605	0.747	0.0363	-0.1047	-0.0205	0.1103	-0.0122	-0.0025	-0.0002	-0.0099	-0.0026	0.0518	0.0032	0.0006	0.0458	0.0059	0.0361	48.6441	5.0251	22.2429
4	1.0213	-0.0518	0.0361	0.8245	-0.0569	0.8428	-0.0227	0.1517	0.0702	-0.0557	0.018	0.1129	0.0262	-0.2183	0.0031	0.0618	-0.0073	-0.0053	0.1134	0.0107	0.0841	30.8131	5.807	9.2549
5	1.4353	-0.2299	0.0161	0.7713	-0.112	1.482	0.0016	0.2093	-0.0215	-0.0386	0.0345	0.056	0.1147	-0.064	-0.0399	0.0895	0.0193	-0.0011	0.0571	-0.0073	0.0526	37.1132	9.8324	3.7283
6	1.0226	0.6725	-0.2314	1.0971	-0.5474	0.9832	0.0169	-0.0019	-0.1142	0.0036	-0.0804	-0.1491	0.0056	0.1425	0.0562	0.0809	0.0125	0.0148	0.0447	-0.0063	0.0865	-1.4466	1.9776	30.4189
7	1.5514	0.0659	0.0528	0.9001	-0.1718	0.8997	0.0057	0.1926	-0.0504	-0.15	-0.0144	-0.0371	0.024	0.0768	-0.001	0.0834	0.0042	0.0082	0.0712	-0.0021	0.0424	-8.2342	6.3018	23.803
8	1.4744	0.0596	0.3832	1.0601	0.0068	0.9091	0.0259	-0.0287	-0.0271	-0.0665	-0.0174	0.0514	-0.0589	-0.0948	-0.0215	0.0536	0.0047	0.0053	0.0342	0.0134	0.0447	-18.4804	4.8754	36.1417
9	1.2831	-0.0049	0.0339	0.751	0.016	0.6586	0.0563	-0.1385	-0.0245	0.0303	-0.0469	-0.1475	0.0225	0.2162	-0.0163	0.0611	0	-0.0079	0.0994	0.0005	0.0731	3.1162	6.3488	41.5973
10	0.7146	0.3579	0.0701	0.2813	0.3112	1.3495	-0.0323	-0.1239	-0.0869	0.0549	0.0641	-0.0358	0.1236	0.1527	-0.0336	0.0733	0.0039	-0.0055	0.0581	0.0156	0.0804	-0.6346	9.4248	45.9815

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 3:32)	A	3 - 32
2	X-RAY DIFFRACTION	2	(chain A and resid 33:58)	A	33 - 58
3	X-RAY DIFFRACTION	3	(chain A and resid 59:184)	A	59 - 184
4	X-RAY DIFFRACTION	4	(chain A and resid 185:253)	A	185 - 253
5	X-RAY DIFFRACTION	5	(chain A and resid 254:284)	A	254 - 284
6	X-RAY DIFFRACTION	6	(chain B and resid 3:33)	B	3 - 33
7	X-RAY DIFFRACTION	7	(chain B and resid 34:119)	B	34 - 119
8	X-RAY DIFFRACTION	8	(chain B and resid 120:184)	B	120 - 184
9	X-RAY DIFFRACTION	9	(chain B and resid 185:248)	B	185 - 248
10	X-RAY DIFFRACTION	10	(chain B and resid 249:284)	B	249 - 284

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