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

ID or keywords:

Entry

Database: PDB / ID: 9mea

Title

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/fructose-1,6-biphosphate 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: 2.83 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 (AMP/fructose-1,6-biphosphate complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 6, 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	9mea.cif.gz	649.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9mea.ent.gz	541.3 KB	Display	PDB format
PDBx/mmJSON format	9mea.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/me/9mea ftp://data.pdbj.org/pub/pdb/validation_reports/me/9mea	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 (5) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #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

194 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)	87.527, 87.527, 475.639
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#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-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#4: 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

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

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: 2.39 Å³/Da / Density % sol: 48.56 %
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 AMP and D-fructose-1,6-biphosphate in crystallant. plate Liu-S-143 AB34. Puck: PSL-0409, Cryo: Direct

Crystal

Density Matthews: 2.39 Å³/Da / Density % sol: 48.56 %

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: 2.83→49.18 Å / Num. obs: 45792 / % possible obs: 100 % / Redundancy: 12.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.181 / R_pim(I) all: 0.053 / R_rim(I) all: 0.189 / Χ²: 1.2 / Net I/σ(I): 15.4 / Num. measured all: 570932
Reflection shell	Resolution: 2.83→2.9 Å / % possible obs: 100 % / Redundancy: 13.3 % / R_merge(I) obs: 1.237 / Num. measured all: 43601 / Num. unique obs: 3272 / CC_1/2: 0.493 / R_pim(I) all: 0.35 / R_rim(I) all: 1.286 / Χ²: 0.8 / Net I/σ(I) obs: 2.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_5438	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.83→48.78 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2421	2280	4.99 %
R_work	0.2038	-	-
obs	0.2057	45656	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.83→48.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12883	0	192	11	13086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	13314
X-RAY DIFFRACTION	f_angle_d	0.744	18049
X-RAY DIFFRACTION	f_dihedral_angle_d	12.607	5015
X-RAY DIFFRACTION	f_chiral_restr	0.044	2062
X-RAY DIFFRACTION	f_plane_restr	0.006	2294

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 (%)
2.83-2.89	0.3619	129	0.307	2625	X-RAY DIFFRACTION	100
2.89-2.96	0.3297	147	0.2929	2651	X-RAY DIFFRACTION	100
2.96-3.03	0.2696	119	0.2745	2671	X-RAY DIFFRACTION	100
3.03-3.11	0.3441	146	0.2844	2663	X-RAY DIFFRACTION	100
3.11-3.21	0.319	130	0.2724	2640	X-RAY DIFFRACTION	100
3.21-3.31	0.284	152	0.2529	2650	X-RAY DIFFRACTION	100
3.31-3.43	0.2525	156	0.2359	2668	X-RAY DIFFRACTION	100
3.43-3.57	0.2683	151	0.2278	2654	X-RAY DIFFRACTION	100
3.57-3.73	0.2845	120	0.214	2706	X-RAY DIFFRACTION	100
3.73-3.92	0.2396	158	0.1989	2684	X-RAY DIFFRACTION	100
3.92-4.17	0.2242	134	0.1804	2736	X-RAY DIFFRACTION	100
4.17-4.49	0.2119	155	0.1662	2667	X-RAY DIFFRACTION	100
4.49-4.94	0.1748	135	0.1656	2772	X-RAY DIFFRACTION	100
4.94-5.66	0.22	129	0.1811	2773	X-RAY DIFFRACTION	100
5.66-7.12	0.2549	166	0.1942	2792	X-RAY DIFFRACTION	100
7.12-48.78	0.203	153	0.1718	3024	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	1.0072	-0.8602	0.1214	0.7711	0.1643	0.7094	0.1925	-0.2395	-0.0079	-0.0349	0.0818	0.1705	0.3749	-0.1442	0.0001	0.5408	-0.1454	-0.0615	0.4485	0.0233	0.4275	24.4776	-27.971	-37.7331
2	0.2418	0.2124	-0.4978	1.0352	0.0027	1.4804	0.0002	0.0741	-0.0248	0.0229	0.0286	0.0669	-0.027	-0.2993	0.0644	0.3297	0.1191	0.0561	0.426	-0.0375	0.3906	23.2713	-2.1804	-15.5122
3	0.228	-0.263	-0.0769	0.5139	-0.1569	0.3295	0.0257	-0.0353	-0.0746	0.2771	0.0511	0.0582	0.564	-0.0954	-0.0013	0.623	-0.0179	0.0186	0.3011	0.0244	0.4656	31.9309	-26.4616	-19.493
4	0.1229	0.1146	0.0625	0.2349	0.2618	0.2117	-0.092	-0.3721	-0.0052	0.0576	0.1112	0.184	0.3134	-0.1589	0.0006	0.5376	0.1278	0.0476	0.5711	-0.0337	0.3852	25.3342	4.5483	4.3207
5	0.0506	-0.1961	0.0033	0.7418	-0.3757	1.1264	0.0466	0.2633	0.0756	-0.3007	-0.0385	0.0947	0.1467	0.1079	-0.0002	0.435	0.0679	-0.0414	0.5938	0.0688	0.367	43.1268	-4.7575	-62.6006
6	0.7724	0.323	0.4094	0.5956	-0.2546	0.5915	0.019	-0.0038	-0.0263	-0.0041	-0.0382	-0.0795	0.0136	0.2729	-0	0.2599	-0.0437	0.0652	0.5748	-0.0475	0.4458	66.3958	5.6439	-38.9212
7	0.3982	0.032	-0.68	0.8513	0.0821	0.8182	0.1554	-0.0851	0.329	-0.2526	-0.01	-0.1385	-0.3713	0.1356	0.177	0.3076	-0.0474	0.0737	0.4214	-0.0024	0.4176	60.02	11.8271	-43.0646
8	0.2837	0.1038	0.0056	0.4311	-0.3228	0.2743	-0.0337	-0.0704	0.1506	0.1849	-0.1109	-0.0321	-0.1077	0.1744	0.0005	0.4435	0.1685	-0.0739	0.691	-0.0937	0.3672	59.1304	0.128	-4.2171
9	0.203	0.1102	0.0905	0.1447	-0.0353	0.1271	-0.1019	0.0691	0.3476	-0.011	0.0366	-0.4369	0.4107	0.6482	0.004	0.5832	0.2528	-0.0405	0.5375	-0.0151	0.5203	55.7075	-13.6683	-7.2547
10	1.0421	-0.4261	-0.1633	1.3197	-0.049	0.7839	-0.0655	-0.1172	0.0251	0.0443	0.1	-0.1286	0.1936	0.2873	0.0225	0.2438	0.1696	-0.0204	0.3814	-0.0388	0.2549	59.2886	-17.2811	-31.2127
11	1.6079	-0.066	-0.89	0.5976	-0.614	1.0696	-0.485	-0.0521	-0.696	0.1196	0.2464	-0.0684	0.874	-0.0181	-0.8273	0.585	0.3961	-0.0522	0.3879	0.0775	0.3136	56.8852	-31.2157	-31.8073
12	0.4274	0.1835	-0.1796	0.6928	-0.033	0.381	0.1936	-0.0689	0.5641	0.2567	0.1352	0.1597	-0.9236	-0.0087	0.0457	0.86	0.0553	0.1694	0.3884	-0.0104	0.7453	41.8342	27.8771	-21.9183
13	0.7715	0.4161	0.0131	1.1142	-0.1672	1.2131	0.0615	0.1685	0.196	0.085	0.0838	0.2572	-0.2552	-0.3432	0.1985	0.2977	0.1304	0.0508	0.5113	0.0855	0.4765	22.1409	10.2027	-40.794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 138 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 139 through 316 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 317 through 383 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 384 through 426 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 155 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 156 through 281 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 282 through 426 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 4 through 125 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 126 through 155 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 156 through 348 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 349 through 426 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 5 through 155 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 156 through 426 )

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