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

ID or keywords:

Entry

Database: PDB / ID: 9mec

Title

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/alpha-D-Glucose-6-phosphate 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: 2.8 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/alpha-D-Glucose-6-phosphate 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

-
Download

PDBx/mmCIF format	9mec.cif.gz	657.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9mec.ent.gz	548.3 KB	Display	PDB format
PDBx/mmJSON format	9mec.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9mec_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	9mec_full_validation.pdf.gz	2.4 MB	Display
Data in XML	9mec_validation.xml.gz	64.9 KB	Display
Data in CIF	9mec_validation.cif.gz	82.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/me/9mec ftp://data.pdbj.org/pub/pdb/validation_reports/me/9mec	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

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)	86.909, 86.909, 473.809
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

-
Protein / Sugars , 2 types, 6 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

#5: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃O₉P / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 7 types, 24 molecules

#2: 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
#3: Chemical	ChemComp-PPV / PYROPHOSPHATE Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.62 %
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 alpha-D-Glucose-6-phosphate in crystallant. plate Liu-S-143 AB34. Puck: PSL-0414, Cryo: Direct

Crystal

Density Matthews: 2.35 Å³/Da / Density % sol: 47.62 %

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 ...

-
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: 2.8→48.94 Å / Num. obs: 46413 / % possible obs: 100 % / Redundancy: 12.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.149 / R_pim(I) all: 0.043 / R_rim(I) all: 0.155 / Χ²: 1.21 / Net I/σ(I): 17.7 / Num. measured all: 592173
Reflection shell	Resolution: 2.8→2.87 Å / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 1.43 / Num. measured all: 44929 / Num. unique obs: 3305 / CC_1/2: 0.506 / R_pim(I) all: 0.401 / R_rim(I) all: 1.486 / Χ²: 0.86 / Net I/σ(I) obs: 2.1

-
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: 2.8→48.94 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2372	2359	5.1 %
R_work	0.1998	-	-
obs	0.2017	46274	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→48.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12899	0	186	7	13092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	13316
X-RAY DIFFRACTION	f_angle_d	0.766	18042
X-RAY DIFFRACTION	f_dihedral_angle_d	12.786	4952
X-RAY DIFFRACTION	f_chiral_restr	0.045	2058
X-RAY DIFFRACTION	f_plane_restr	0.007	2299

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 (%)
2.8-2.86	0.3549	154	0.2918	2484	X-RAY DIFFRACTION	100
2.86-2.92	0.3875	143	0.2854	2504	X-RAY DIFFRACTION	100
2.92-2.99	0.3177	132	0.2713	2557	X-RAY DIFFRACTION	100
2.99-3.06	0.2914	115	0.2764	2526	X-RAY DIFFRACTION	100
3.06-3.14	0.3015	145	0.267	2527	X-RAY DIFFRACTION	100
3.14-3.24	0.3266	159	0.2673	2535	X-RAY DIFFRACTION	100
3.24-3.34	0.2817	164	0.2365	2515	X-RAY DIFFRACTION	100
3.34-3.46	0.296	123	0.2232	2548	X-RAY DIFFRACTION	100
3.46-3.6	0.2531	131	0.2102	2567	X-RAY DIFFRACTION	100
3.6-3.76	0.2588	130	0.2028	2566	X-RAY DIFFRACTION	100
3.76-3.96	0.2206	124	0.1925	2600	X-RAY DIFFRACTION	100
3.96-4.21	0.1961	150	0.1674	2537	X-RAY DIFFRACTION	100
4.21-4.53	0.1812	122	0.161	2622	X-RAY DIFFRACTION	100
4.53-4.99	0.1789	136	0.1653	2613	X-RAY DIFFRACTION	100
4.99-5.71	0.2769	131	0.1856	2650	X-RAY DIFFRACTION	100
5.71-7.19	0.2289	140	0.2047	2705	X-RAY DIFFRACTION	100
7.19-48.94	0.1965	160	0.1794	2859	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	1.4179	-1.8763	0.2619	1.337	-0.6811	1.1863	0.0759	-0.0937	0.1317	-0.5395	0.3664	0.5249	0.843	-0.2544	0.2616	0.8548	-0.2591	-0.2395	0.5448	0.0696	0.6644	24.0855	-27.7927	-38.0185
2	0.4776	-0.1881	-0.4525	1.5565	0.9053	1.6426	-0.0833	0.1349	0.1308	0.1023	0.1163	0.125	0.1	-0.3406	0.0214	0.4392	0.0779	0.0345	0.5691	0.0194	0.4764	23.0424	-4.1661	-16.2344
3	0.2372	-0.636	-0.2064	0.8908	-0.1399	0.5246	-0.1849	-0.2135	-0.1022	0.3179	0.246	0.2562	0.3442	-0.201	0.1268	0.6221	0.0674	0.0069	0.5233	0.0153	0.5823	28.9102	-14.1555	-9.7289
4	1.1352	-1.1578	0.1642	1.0678	-0.8375	2.662	0.2518	0.23	-0.0296	-0.3839	-0.1506	0.014	0.3661	0.0772	0.0125	0.6132	0.0149	-0.0805	0.6069	0.0246	0.4661	42.9477	-5.088	-62.5442
5	0.2928	0.1702	0.0664	1.0016	0.2103	1.5229	0.0235	-0.0173	0.1591	-0.1561	0.1147	-0.2512	-0.1965	0.3577	0.1115	0.3326	-0.0898	0.036	0.6284	-0.0247	0.5792	62.6287	8.7041	-40.9819
6	0.8574	0.3505	-0.4342	0.3108	-0.6956	0.7245	-0.239	-0.0629	0.0361	0.4891	0.0951	-0.1406	-0.2148	0.3231	0.0105	0.6164	0.2015	-0.162	0.8388	-0.1671	0.5781	58.7413	0.0021	-4.0815
7	0.0469	-0.0112	0.1324	0.046	-0.1257	0.4339	0.0817	-0.1262	0.3533	0.1684	0.2088	-0.5954	0.1509	0.4123	0.0433	0.9218	0.2824	-0.1264	0.6517	-0.0209	0.6284	55.4357	-13.8873	-7.1138
8	1.0352	-0.4058	-0.1959	1.2522	0.3078	1.4593	-0.0873	-0.0639	0.1659	0.0829	0.1127	-0.163	0.2735	0.3898	-0.0017	0.5006	0.1848	-0.058	0.586	-0.0716	0.4565	58.9843	-17.5155	-31.1437
9	1.5243	-1.1621	-0.3955	1.191	-0.4297	1.2104	-0.6059	-0.1038	-0.5665	-0.0222	0.3356	-0.0742	0.9388	0.0308	-0.6673	0.7485	0.3123	-0.1037	0.6271	0.014	0.4443	56.6325	-31.4293	-31.672
10	0.8025	0.4322	-0.4497	0.7619	0.2781	1.29	0.073	0.0955	0.2643	0.2376	0.1599	-0.0684	-0.7723	0.0576	0.0702	0.9129	0.0485	0.0875	0.4392	-0.0148	0.7686	42.2161	27.473	-18.92
11	0.4165	0.8012	0.205	1.1009	0.0383	1.5589	0.0597	0.2543	0.1109	0.1399	0.1589	0.3622	-0.2157	-0.6323	0.3278	0.4131	0.1299	-0.005	0.7193	0.1534	0.6969	21.4939	8.8744	-36.6153
12	0.4065	0.6913	-0.0685	0.2532	0.0576	1.0488	0.0543	0.6019	0.5203	-0.2067	0.1898	0.1953	-0.7875	0.2681	0.0399	0.7552	0.0148	0.0384	0.4995	0.1372	0.9412	38.034	24.9472	-39.6806
13	0.5912	0.0304	-0.1638	0.4422	0.084	0.2495	0.0177	0.5702	-0.0788	-0.1469	-0.0492	0.0031	-0.1664	-1.2601	-0.1352	0.5246	0.017	-0.1455	1.3695	0.2161	0.9012	9.2025	1.9876	-54.9796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 126 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 127 through 316 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 317 through 426 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 155 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 156 through 426 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 4 through 125 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 126 through 155 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 156 through 348 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 349 through 426 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 5 through 125 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 126 through 316 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 317 through 384 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 385 through 426 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / Sugars , 2 types, 6 molecules ABCD

-
Non-polymers , 7 types, 24 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein / Sugars , 2 types, 6 molecules ABCD

-Non-polymers , 7 types, 24 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / Sugars , 2 types, 6 molecules ABCD

-
Non-polymers , 7 types, 24 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi