PDB-9mf6: Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phospho...

ID or keywords:

Entry

Database: PDB / ID: 9mf6

Title

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)

Components

Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 / Trichomonas vaginalis

Function / homology

Function and homology information

diphosphate-fructose-6-phosphate 1-phosphotransferase / diphosphate-fructose-6-phosphate 1-phosphotransferase activity / phosphofructokinase activity / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / response to glucose / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 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 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)
Authors: Seibold, S. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 9, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mf6.cif.gz	641.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9mf6.ent.gz	532.7 KB	Display	PDB format
PDBx/mmJSON format	9mf6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mf/9mf6 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/9mf6	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	#50 - Feb 2004 Glycolytic Enzymes similarity (4) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

B: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

C: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

D: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

hetero molecules

193 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	86.960, 86.960, 473.874
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein

Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 / 6-phosphofructokinase / pyrophosphate dependent 1 / PPi-dependent phosphofructokinase 1 / PPi-PFK 1 ...

Mass: 47625.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trichomonas vaginalis G3 (eukaryote) / Gene: Pfk1, TVAG_430830 / Plasmid: TrvaA.00429.d.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O61068, diphosphate-fructose-6-phosphate 1-phosphotransferase

#2: Sugar

ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose

Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₁₁O₈P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 34 molecules

#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PPV / PYROPHOSPHATE Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄O₇P₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.35 Å³/Da / Density % sol: 47.69 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. 5 hour soak in 2 mM ...Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. 5 hour soak in 2 mM ADP and 5-O-phosphono-alpha-D-ribofuranose in crystallant. plate Liu-S-143 AB34. Puck: PSL-0412, Cryo: Direct

Crystal

Density Matthews: 2.35 Å³/Da / Density % sol: 47.69 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. 5 hour soak in 2 mM ...

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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: Sep 28, 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: 2.65→48.96 Å / Num. obs: 54628 / % possible obs: 100 % / Redundancy: 12.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.028 / R_rim(I) all: 0.1 / Χ²: 1 / Net I/σ(I): 15.1 / Num. measured all: 690768
Reflection shell	Resolution: 2.65→2.73 Å / % possible obs: 100 % / Redundancy: 13.7 % / R_merge(I) obs: 1.597 / Num. measured all: 60604 / Num. unique obs: 4410 / CC_1/2: 0.674 / R_pim(I) all: 0.445 / R_rim(I) all: 1.658 / Χ²: 1.02 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	dev_5533	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→48.96 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2628	2728	5.01 %
R_work	0.2077	-	-
obs	0.2104	54470	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.65→48.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12432	0	158	28	12618

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12830
X-RAY DIFFRACTION	f_angle_d	0.512	17455
X-RAY DIFFRACTION	f_dihedral_angle_d	13.638	4634
X-RAY DIFFRACTION	f_chiral_restr	0.041	2053
X-RAY DIFFRACTION	f_plane_restr	0.004	2235

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 (%)
2.65-2.7	0.3533	149	0.308	2668	X-RAY DIFFRACTION	100
2.7-2.75	0.3809	126	0.2891	2655	X-RAY DIFFRACTION	100
2.75-2.81	0.3494	145	0.2714	2700	X-RAY DIFFRACTION	100
2.81-2.87	0.3387	136	0.2625	2632	X-RAY DIFFRACTION	100
2.87-2.93	0.3309	152	0.262	2660	X-RAY DIFFRACTION	100
2.93-3.01	0.3253	149	0.2604	2682	X-RAY DIFFRACTION	100
3.01-3.09	0.3204	162	0.2828	2666	X-RAY DIFFRACTION	100
3.09-3.18	0.3825	157	0.296	2628	X-RAY DIFFRACTION	100
3.18-3.28	0.3327	131	0.2871	2705	X-RAY DIFFRACTION	100
3.28-3.4	0.3313	130	0.2379	2708	X-RAY DIFFRACTION	100
3.4-3.54	0.2832	128	0.2102	2713	X-RAY DIFFRACTION	100
3.54-3.7	0.279	147	0.2151	2695	X-RAY DIFFRACTION	100
3.7-3.89	0.2944	133	0.2119	2728	X-RAY DIFFRACTION	100
3.89-4.13	0.2456	147	0.177	2747	X-RAY DIFFRACTION	100
4.13-4.45	0.2252	156	0.1668	2705	X-RAY DIFFRACTION	100
4.45-4.9	0.2071	133	0.1644	2777	X-RAY DIFFRACTION	100
4.9-5.61	0.2343	129	0.195	2810	X-RAY DIFFRACTION	100
5.61-7.06	0.2826	164	0.2217	2812	X-RAY DIFFRACTION	100
7.07-48.96	0.2136	154	0.1862	3051	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	1.7411	-1.1242	0.1995	3.1062	-0.8752	2.1466	-0.0508	-0.0826	0.1767	-0.4317	0.2943	0.2958	0.8443	-0.0046	-0.1354	0.9377	-0.1554	-0.1174	0.6385	-0.0078	0.6211	28.0549	-25.1095	-40.3198
2	0.5878	-0.0766	0.272	2.433	0.4049	3.3319	-0.3897	0.4664	-0.0241	0.1926	0.5327	1.2521	1.0877	-1.1138	-0.2485	1.1167	-0.3909	-0.053	0.9389	0.16	1.0631	17.9073	-31.8806	-33.3374
3	2.0167	-0.8394	-1.6164	8.098	0.0772	2.4057	-0.6475	0.1325	0.025	0.2222	0.4713	0.1343	0.3009	-0.2526	0.0634	0.9544	-0.1111	0.063	0.703	0.0201	0.7313	28.0665	-25.8269	-23.8036
4	1.9522	0.0195	-0.7034	2.5666	1.1674	2.602	-0.091	0.1504	0.0272	0.0214	0.1089	0.1306	0.0769	-0.3615	-0.0109	0.523	0.0888	0.0281	0.6354	0.0669	0.5676	22.3179	-0.6447	-14.9671
5	0.2994	-1.1599	-0.8855	4.0002	2.3386	3.2852	-0.2435	-0.1412	-0.3103	0.5569	0.0508	0.4495	0.9496	-0.0178	0.2366	0.9329	-0.0135	-0.042	0.6123	0.0108	0.8852	32.2097	-25.8028	-19.4064
6	3.3305	-0.8002	-1.1752	2.5265	2.0068	3.7562	-0.2367	-0.6058	0.5094	0.7968	0.2116	-0.3775	0.1628	-0.0425	0.0562	0.781	0.2082	0.0257	0.6119	0.0314	0.5854	24.4149	4.4268	4.6218
7	2.9841	-2.3362	-0.0318	2.4745	0.8647	3.7815	0.1693	0.4001	0.1271	-0.4898	0.0307	0.0763	0.3692	0.1534	-0.2011	0.713	-0.0286	-0.07	0.7733	0.049	0.5451	42.09	-7.7219	-62.9134
8	3.6212	0.1458	1.6896	2.4709	0.3749	3.7909	-0.1685	0.7409	0.1905	-0.4878	0.1638	-0.6605	-0.6503	0.1693	0.1408	0.9363	-0.0855	0.069	0.928	0.2506	0.8186	46.4679	5.9364	-58.9774
9	1.4749	0.5415	-0.2183	1.2627	-0.0529	2.0163	-0.0878	-0.1262	0.0907	-0.0926	0.0887	-0.2145	-0.0297	0.4797	-0.0225	0.4948	-0.0542	0.019	0.8377	-0.0569	0.7867	65.6522	5.5439	-38.0554
10	1.7606	-0.3972	-0.53	1.4396	0.2917	3.29	0.0077	-0.0185	0.4888	-0.2817	0.0652	-0.1042	-0.1537	-0.2063	0.018	0.4991	-0.009	0.0286	0.5536	0.0273	0.598	51.6523	4.8845	-48.9798
11	1.9426	0.047	-0.3432	1.129	-0.6	1.6881	-0.1496	-0.2158	-0.0105	-0.1709	0.0324	-0.0744	-0.4961	-0.1297	-0.0145	0.6411	-0.1524	0.1005	0.6945	-0.0004	0.7406	62.3709	19.3335	-40.2346
12	1.4435	0.6526	0.0867	0.9494	1.3062	3.5515	0.164	-0.4304	0.8537	-0.2295	-0.0687	-0.0469	-0.6434	0.5215	-0.1274	0.7806	-0.3041	-0.0773	1.0006	-0.0079	1.0924	77.6004	19.3449	-29.2228
13	2.2117	0.291	0.4255	0.6142	-0.8039	1.6271	0.0611	0.2555	0.0373	0.2298	-0.0415	0.0696	-0.2877	0.1099	-0.0579	0.6723	0.1586	-0.1055	0.6741	-0.0816	0.5738	54.2434	2.8377	-5.0474
14	1.6241	0.7101	0.7401	0.4019	-0.0742	2.9611	-0.1248	-0.1892	-0.2473	0.3312	0.1392	-0.5008	0.6363	0.8624	-0.097	0.8893	0.2785	-0.1532	1.2197	-0.1274	0.9251	64.0024	-3.8741	-2.7942
15	2.554	-0.1656	0.0273	2.232	1.5376	3.5047	-0.1676	-0.1037	0.1978	0.0994	0.1179	-0.3188	0.3233	0.4634	-0.0153	1.0628	0.2899	-0.1025	0.8088	0.0343	0.795	55.1857	-13.9186	-7.5646
16	2.0399	0.1479	-1.8671	2.5098	0.6628	2.8237	-0.1626	-0.2016	0.0351	0.247	0.1647	-0.0192	0.3482	0.3022	-0.0427	0.5755	0.1507	-0.0537	0.593	-0.0736	0.5002	55.8457	-20.6195	-36.2778
17	2.096	-1.8635	-0.0209	2.573	0.1939	0.8591	-0.0874	-0.1739	0.4146	-0.0441	0.1349	-0.3904	0.0464	0.4333	-0.078	0.6008	0.1441	0.0072	0.8548	-0.0695	0.5997	66.2658	-16.4361	-35.9798
18	1.0877	1.3313	0.8264	1.7519	0.2721	6.3549	0.2426	-0.3313	-0.4865	0.355	0.4554	-0.162	1.0364	0.6542	-0.6278	0.8852	0.2824	-0.0933	0.8445	-0.0454	0.5733	48.2566	-13.6436	-4.0617
19	2.5077	0.3145	-0.1822	1.2892	-1.1598	1.1727	-0.663	-0.233	-0.3667	-0.4085	0.3058	0.1453	1.2299	0.0188	0.0064	0.9177	0.3723	-0.0201	0.737	0.0052	0.5958	53.7129	-30.8265	-29.1726
20	0.6862	-0.3849	1.5481	2.1249	0.1737	4.0012	-0.2039	0.3999	-0.1033	-0.3572	-0.1711	-0.0475	0.0818	0.1805	0.3646	1.0639	0.2248	0.0658	0.7789	-0.1079	0.6614	60.2723	-36.5289	-46.8433
21	2.0303	0.3381	0.2476	1.6326	0.5311	2.4689	-0.1859	0.2264	0.1683	0.2557	0.1146	0.3393	-0.5157	-0.0946	0.017	0.8349	0.0184	0.0398	0.5458	-0.0092	0.9032	43.0082	25.88	-17.937
22	3.614	0.8126	0.7628	1.4898	1.4253	1.9054	-0.0236	0.0697	1.1904	0.1058	0.3235	0.5302	-0.935	-0.3306	-0.2322	1.2753	0.1404	0.1992	0.7412	0.2601	1.2233	38.9013	29.8296	-28.7673
23	2.6845	0.5444	0.4386	1.2526	0.3534	1.6837	0.0808	0.1033	0.2733	0.0166	0.1154	0.0367	-0.2773	-0.4454	-0.1695	0.5506	0.1031	0.0017	0.809	0.138	0.6655	23.5108	8.7794	-36.8796
24	2.4244	1.1943	1.8312	1.3122	0.7751	1.968	-0.5232	0.5388	0.7586	-0.891	0.3929	0.49	-0.7065	-0.0252	0.2501	0.6137	0.1953	0.0258	0.6686	0.1936	0.87	30.4395	22.3873	-44.8074
25	3.499	-1.574	0.4951	2.6497	0.3807	3.3396	0.0778	1.3781	0.1874	-0.8014	-0.1136	0.6157	0.1253	-1.409	0.0403	0.6281	0.0875	-0.1005	1.5068	0.2399	0.8765	9.2258	1.9511	-54.8354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 85 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 through 155 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 156 through 316 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 317 through 384 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 385 through 426 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 126 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 127 through 155 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 156 through 281 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 282 through 363 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 364 through 395 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 396 through 426 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 4 through 73 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 74 through 126 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 127 through 155 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 156 through 236 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 237 through 316 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 317 through 357 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 358 through 395 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 396 through 426 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 5 through 102 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 103 through 155 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 156 through 348 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 349 through 384 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 385 through 426 )

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Protein / Sugars , 2 types, 8 molecules ABCD

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-Non-polymers , 4 types, 34 molecules

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Protein / Sugars , 2 types, 8 molecules ABCD

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Non-polymers , 4 types, 34 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Yorodumi