PDB-9dqm: Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotra...

ID or keywords:

Entry

Database: PDB / ID: 9dqm

Title

Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP bound)

Components

Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

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: 2.2 Å

Authors

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 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9dqm.cif.gz	329.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9dqm.ent.gz	267.6 KB	Display	PDB format
PDBx/mmJSON format	9dqm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dqm_validation.pdf.gz	554.2 KB	Display	wwPDB validaton report
Full document	9dqm_full_validation.pdf.gz	558.9 KB	Display
Data in XML	9dqm_validation.xml.gz	17.7 KB	Display
Data in CIF	9dqm_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/9dqm ftp://data.pdbj.org/pub/pdb/validation_reports/dq/9dqm	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

hetero molecules

96.1 kDa, 2 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)	90.584, 90.584, 376.753
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-634- HOH

#1: Protein	Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 / 6-phosphofructokinase / pyrophosphate dependent 1 / PPi-dependent phosphofructokinase 1 / PPi-PFK 1 ...6-phosphofructokinase / pyrophosphate dependent 1 / PPi-dependent phosphofructokinase 1 / PPi-PFK 1 / Pyrophosphate-dependent 6-phosphofructose-1-kinase 1 Mass: 47625.797 Da / Num. of mol.: 2 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: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.49 %
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. 2mM pyrophosphate ...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. 2mM pyrophosphate added prior to screening. However, only phosphate and AMP were observed in the acitive site. The AMP is likely acquired from the expression host. SS: Clover position A2. Puck: PSL-1510, Cryo: Direct

Crystal

Density Matthews: 2.34 Å³/Da / Density % sol: 47.49 %

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. 2mM pyrophosphate ...

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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: Jul 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: 2.2→49.02 Å / Num. obs: 47899 / % possible obs: 100 % / Redundancy: 35.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.014 / R_rim(I) all: 0.086 / Χ²: 1 / Net I/σ(I): 25 / Num. measured all: 1689888
Reflection shell	Resolution: 2.2→2.27 Å / % possible obs: 99.7 % / Redundancy: 20.8 % / R_merge(I) obs: 1.95 / Num. measured all: 84063 / Num. unique obs: 4051 / CC_1/2: 0.685 / R_pim(I) all: 0.434 / R_rim(I) all: 1.999 / Χ²: 1.02 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5462: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→45.29 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2636	2357	4.94 %
R_work	0.2113	-	-
obs	0.2138	47753	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→45.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6133	0	56	84	6273

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6312
X-RAY DIFFRACTION	f_angle_d	0.791	8599
X-RAY DIFFRACTION	f_dihedral_angle_d	15.682	2211
X-RAY DIFFRACTION	f_chiral_restr	0.048	1013
X-RAY DIFFRACTION	f_plane_restr	0.008	1105

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 (%)
2.2-2.24	0.3224	131	0.2985	2585	X-RAY DIFFRACTION	99
2.24-2.29	0.3062	137	0.2761	2591	X-RAY DIFFRACTION	100
2.29-2.35	0.3433	130	0.2488	2610	X-RAY DIFFRACTION	100
2.35-2.41	0.351	135	0.2378	2612	X-RAY DIFFRACTION	100
2.41-2.47	0.3014	141	0.2461	2629	X-RAY DIFFRACTION	100
2.47-2.54	0.2957	129	0.2576	2606	X-RAY DIFFRACTION	100
2.54-2.63	0.4071	142	0.2899	2630	X-RAY DIFFRACTION	100
2.63-2.72	0.3519	116	0.297	2653	X-RAY DIFFRACTION	100
2.72-2.83	0.3125	140	0.2727	2653	X-RAY DIFFRACTION	100
2.83-2.96	0.3133	145	0.2473	2626	X-RAY DIFFRACTION	100
2.96-3.11	0.2946	144	0.2591	2657	X-RAY DIFFRACTION	100
3.11-3.31	0.2984	136	0.2607	2658	X-RAY DIFFRACTION	100
3.31-3.56	0.278	139	0.2154	2682	X-RAY DIFFRACTION	100
3.56-3.92	0.2353	154	0.1873	2699	X-RAY DIFFRACTION	100
3.92-4.49	0.1908	167	0.1688	2702	X-RAY DIFFRACTION	100
4.49-5.65	0.1997	124	0.1744	2809	X-RAY DIFFRACTION	100
5.65-45.29	0.2993	147	0.195	2994	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	2.7827	0.1416	1.4281	3.2871	-0.4475	3.4195	0.0997	-0.4043	-0.4495	0.116	-0.1248	0.2048	1.0104	-0.0847	0.0764	0.7597	0.0052	0.0358	0.5882	0.2502	0.5552	-18.2808	11.5773	-15.7966
2	4.1982	-1.9489	0.6986	6.9992	-2.0002	3.9555	0.44	-0.4719	-0.2999	0.3393	-0.2836	0.8405	0.2314	-0.5129	-0.0273	0.7612	-0.1081	0.026	0.7956	0.1637	0.5528	-25.3544	23.0996	-7.2346
3	1.3532	-0.2823	-0.376	3.1729	0.1174	2.5335	-0.1962	0.0188	-0.2508	0.014	-0.0193	0.4035	0.3335	-0.6259	0.1917	0.2818	-0.0831	0.0113	0.6743	0.0304	0.4924	-46.9425	33.7917	-20.371
4	2.4238	-0.6291	0.4655	1.7185	-0.3328	1.8575	-0.1068	-0.3631	-0.0119	0.2516	-0.0623	0.0596	0.3708	-0.2019	0.119	0.5073	-0.0803	0.0224	0.6075	0.1118	0.4067	-31.5032	27.7008	-14.801
5	3.2274	0.1265	0.2521	2.984	-1.1755	3.7126	-0.3272	-0.4183	0.5591	0.4275	0.1322	0.4231	-0.2951	-0.7701	0.0616	0.4058	0.024	0.0515	0.8786	-0.0377	0.5993	-53.0676	44.8928	-12.4598
6	3.2406	-0.6671	-0.8996	2.7216	-0.0945	3.0219	-0.2095	-0.3418	0.561	-0.1519	0.0817	0.0028	-0.733	-0.3218	0.1222	0.6282	0.0982	-0.1664	0.5234	-0.0248	0.6185	-32.6126	63.1948	-19.8787
7	1.5066	-1.0376	-1.8279	3.6719	1.7638	2.4506	0.1301	-0.6569	0.7263	-0.1518	0.2559	-0.5824	-0.3656	0.4016	-0.3595	0.8281	-0.1569	-0.2108	0.6845	-0.0946	0.7865	-22.1259	73.3055	-14.486
8	5.2108	-0.2066	0.9658	2.5538	0.2855	4.0615	-0.2755	-0.4968	0.351	0.7242	0.1498	-0.2466	-0.441	0.7158	0.1267	0.7779	-0.1058	-0.1431	0.7245	-0.0337	0.5903	-24.3225	60.4175	-8.6123
9	1.3722	-0.1141	0.3158	2.7324	0.3582	3.2706	-0.1201	-0.1869	0.1198	0.0694	0.0441	-0.2992	-0.317	0.6405	0.0599	0.3208	-0.09	-0.0868	0.685	0.1924	0.5012	-0.8663	42.2603	-20.1313
10	3.0899	-2.4558	-1.4266	3.181	2.9229	4.0044	0.1045	0.3534	0.2385	-1.3208	0.1642	-0.3867	-0.4363	0.6796	-0.3214	0.4613	-0.2268	-0.0449	0.9069	0.2238	0.7372	6.3588	49.7366	-24.5535
11	3.3275	-0.7479	-0.5581	1.3437	0.4392	1.8938	-0.2459	-0.5238	0.0841	0.333	0.0348	0.044	-0.4366	-0.028	0.156	0.5622	0.0203	-0.0912	0.6086	0.0726	0.4148	-22.4609	52.0625	-11.841
12	3.8491	0.8323	0.2864	1.4648	0.5325	0.6573	-0.3083	-0.6682	-0.5222	0.6061	0.1894	-0.3419	0.3805	0.798	-0.0517	0.4929	0.1208	-0.1416	1.0937	0.2204	0.5913	6.059	32.3538	-11.912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 123 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 124 through 155 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 156 through 281 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 282 through 364 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 365 through 426 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 78 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 79 through 102 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 103 through 155 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 156 through 270 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 271 through 297 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 298 through 367 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 368 through 426 )

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