PDB-9o8j: Crystal structure of Phosphoglycerate mutase from Trichomonas vag...

ID or keywords:

Entry

Database: PDB / ID: 9o8j

Title

Crystal structure of Phosphoglycerate mutase from Trichomonas vaginalis (sulfate bound)

Components

Phosphoglycerate mutase

Keywords

ISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Trichomonas vaginalis / Phosphoglycerate mutase

Function / homology

Function and homology information

phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / canonical glycolysis / cytosol
Similarity search - Function

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Phosphoglycerate mutase from Trichomonas vaginalis (sulfate bound)
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.

History

Deposition	Apr 16, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9o8j.cif.gz	208.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9o8j.ent.gz	167.8 KB	Display	PDB format
PDBx/mmJSON format	9o8j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9o8j_validation.pdf.gz	450.4 KB	Display	wwPDB validaton report
Full document	9o8j_full_validation.pdf.gz	454.9 KB	Display
Data in XML	9o8j_validation.xml.gz	22.1 KB	Display
Data in CIF	9o8j_validation.cif.gz	28 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/9o8j ftp://data.pdbj.org/pub/pdb/validation_reports/o8/9o8j	HTTPS FTP

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Related structure data

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	#257 - May 2021 Fetal Hemoglobin similarity (8) #50 - Feb 2004 Glycolytic Enzymes similarity (8) #225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Phosphoglycerate mutase

B: Phosphoglycerate mutase

hetero molecules

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

1

A: Phosphoglycerate mutase

hetero molecules

A: Phosphoglycerate mutase

hetero molecules

defined by author&software
Evidence: gel filtration
62 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglycerate mutase

hetero molecules

B: Phosphoglycerate mutase

hetero molecules

defined by author&software
60.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.361, 95.803, 73.521
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-428- HOH

#1: Protein	Phosphoglycerate mutase Mass: 29850.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_165570 / Plasmid: TrvaA.01013.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A2DUN8, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.85 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystal Screen HT F11: 1.60M A/S, 0.10M MES, pH 6.5, 10% 1,4-dioxane. TrvaA.01013.a.B1.PW39315 at 18.8 mg/mL. plate 19517 well F11 drop 1, Puck: PSL-0611, Cryo: 2.5M Li2SO4.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 14, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.05→47.9 Å / Num. obs: 41670 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.125 / R_pim(I) all: 0.036 / R_rim(I) all: 0.13 / Χ²: 1.06 / Net I/σ(I): 14.3 / Num. measured all: 549189
Reflection shell	Resolution: 2.05→2.1 Å / % possible obs: 100 % / Redundancy: 13.5 % / R_merge(I) obs: 1.528 / Num. measured all: 40923 / Num. unique obs: 3028 / CC_1/2: 0.523 / R_pim(I) all: 0.429 / R_rim(I) all: 1.588 / Χ²: 0.9 / Net I/σ(I) obs: 1.9

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Processing

Software

Name	Version	Classification
PHENIX	dev_5660	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→47.9 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2393	2100	5.05 %
R_work	0.2055	-	-
obs	0.2071	41603	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3721	0	90	99	3910

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3902
X-RAY DIFFRACTION	f_angle_d	0.494	5286
X-RAY DIFFRACTION	f_dihedral_angle_d	15.553	1452
X-RAY DIFFRACTION	f_chiral_restr	0.039	565
X-RAY DIFFRACTION	f_plane_restr	0.004	660

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 (%)
2.05-2.1	0.2754	138	0.2706	2580	X-RAY DIFFRACTION	100
2.1-2.15	0.3084	142	0.2624	2593	X-RAY DIFFRACTION	100
2.15-2.21	0.3138	132	0.2566	2604	X-RAY DIFFRACTION	100
2.21-2.27	0.3164	160	0.2537	2581	X-RAY DIFFRACTION	100
2.27-2.35	0.2496	145	0.2329	2575	X-RAY DIFFRACTION	100
2.35-2.43	0.2735	124	0.2423	2632	X-RAY DIFFRACTION	100
2.43-2.53	0.244	149	0.2249	2603	X-RAY DIFFRACTION	100
2.53-2.64	0.2242	150	0.2289	2589	X-RAY DIFFRACTION	100
2.64-2.78	0.2629	145	0.2188	2620	X-RAY DIFFRACTION	100
2.78-2.96	0.2643	145	0.2418	2636	X-RAY DIFFRACTION	100
2.96-3.18	0.283	137	0.23	2640	X-RAY DIFFRACTION	100
3.18-3.5	0.262	139	0.2055	2624	X-RAY DIFFRACTION	100
3.51-4.01	0.2206	144	0.1729	2680	X-RAY DIFFRACTION	100
4.01-5.05	0.1797	120	0.1614	2711	X-RAY DIFFRACTION	100
5.05-47.9	0.2182	130	0.2022	2835	X-RAY DIFFRACTION	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	4.4491	-1.5937	-0.4039	1.9619	2.0798	2.7231	-0.0334	0.209	-0.8986	0.4592	-0.1773	-0.4326	0.1294	0.1575	0.1688	0.4274	0.1141	-0.01	0.2167	0.0551	0.4482	15.338	-14.9531	-0.0857
2	7.8144	1.0611	3.0183	2.2304	1.2761	7.2181	0.2448	-0.7993	-0.4675	0.7585	-0.1394	0.2044	0.9864	-0.4434	-0.0939	0.508	-0.0159	0.0353	0.3155	0.0267	0.3903	-9.2345	-15.7585	13.7686
3	6.7754	0.1431	-0.7574	2.6184	-0.1812	4.2504	0.1914	-0.618	-0.0663	0.252	-0.0834	-0.2531	0.223	0.3858	-0.0766	0.2945	0.0229	-0.0552	0.1685	-0.0106	0.363	6.7056	-9.188	9.2604
4	1.6599	0.4501	0.2463	1.7754	0.0856	2.9006	0.0594	0.0329	0.1633	0.157	-0.1074	-0.2295	-0.1791	0.0918	0.088	0.2425	0.034	-0.0165	0.1882	-0.0137	0.3346	1.059	-5.4378	4.2853
5	3.9263	1.6117	1.3016	5.4471	3.7147	2.5465	0.3356	-1.2459	-0.8539	1.2262	-0.4031	-0.0753	1.2641	-0.0605	0.2287	0.7399	-0.119	0.0239	0.4796	0.1134	0.7012	-15.9915	-25.5085	9.5406
6	8.5363	-0.891	-0.8658	4.082	-0.5328	3.5672	0.0095	-1.0267	-0.9254	-0.3493	0.1768	-0.4463	0.6373	0.1278	-0.2454	0.4832	-0.1146	-0.0189	0.4142	0.0237	0.7516	-15.9553	-28.9373	4.3546
7	6.6715	2.4118	-3.0385	3.3411	0.0991	3.8411	0.0282	0.5253	0.2192	-0.1081	-0.0414	0.4136	0.0267	-0.4499	0.0372	0.2511	-0.0112	-0.0559	0.2726	-0.027	0.3718	-11.4129	-14.9607	-4.8795
8	5.9729	0.4799	-2.8375	2.3012	0.968	4.8247	0.0064	0.3532	-0.5111	-0.0626	-0.0327	-0.0669	0.2353	-0.0208	0.0566	0.2888	0.0761	-0.0396	0.2257	-0.0114	0.3246	4.8636	-16.8423	-3.3704
9	4.0845	2.2265	1.1636	2.1547	0.3882	2.9726	0.8151	-0.6489	-1.1575	1.0965	0.0081	0.379	0.4156	-0.5279	-0.5736	1.0747	-0.0492	-0.0589	0.605	0.0743	1.0296	2.4719	-29.128	4.0634
10	7.7296	-0.398	-1.5398	9.4358	0.4108	5.9625	0.4112	0.2553	-0.7487	0.1565	-0.1637	-0.151	0.6188	0.5451	-0.1653	0.4057	0.1767	-0.0544	0.2973	-0.0018	0.5135	13.8321	-20.0524	-1.6104
11	4.2458	2.0009	1.3607	1.7928	2.4466	4.2687	-0.262	-0.0314	0.7294	-0.4092	0.0747	0.4149	-0.887	0.8323	0.3525	0.7886	-0.501	-0.1413	1.0354	0.0425	0.4435	14.4796	15.5502	-36.8223
12	2.9241	-0.2039	1.227	5.6454	-0.0634	6.6334	-0.1109	-0.1776	0.1325	0.5471	-0.0896	-0.1976	-0.1597	1.198	0.2172	0.5381	-0.0456	0.0009	0.6611	0.0682	0.2816	10.464	0.0956	-26.0385
13	0.8385	-0.4279	0.9291	3.2409	-0.6325	1.0417	-0.3892	-0.2151	-0.0269	0.7875	0.1241	-0.5809	0.1655	1.267	0.3207	0.7794	0.2622	-0.0257	1.1493	0.1139	0.5148	16.5009	-9.2553	-31.6627
14	1.1844	0.2502	0.6455	5.1061	-0.2598	2.0331	0.1732	0.946	-0.5195	0.7568	-0.0478	-0.8292	0.1661	0.7046	-0.101	0.8629	0.341	-0.0148	1.2476	0.0962	0.7727	28.4799	-16.7647	-32.6044
15	2.34	-0.7757	0.2512	5.7779	-0.712	4.8228	-0.0332	0.274	-0.2117	-0.1294	-0.1515	-0.2948	0.5391	1.7118	0.1945	0.6318	0.1206	0.0308	1.0993	0.0943	0.3821	15.5503	-4.6548	-41.0529
16	2.7418	-0.9358	1.3667	2.9329	-1.0952	3.5754	-0.2354	-0.7473	-0.2817	-0.1526	0.3271	-0.3582	-0.765	0.7767	-0.3527	0.8974	-0.6598	-0.1363	1.5797	0.1232	0.5983	20.7783	11.8622	-35.8364

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 93 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 94 through 114 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 138 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 139 through 173 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 174 through 201 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 202 through 218 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 219 through 238 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 4 through 16 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 17 through 80 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 81 through 114 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 115 through 138 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 139 through 201 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 202 through 239 )

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