PDB-5et6: Human muscle fructose-1,6-bisphosphatase in inactive T-state in c...

ID or keywords:

Entry

Database: PDB / ID: 5et6

Title

Human muscle fructose-1,6-bisphosphatase in inactive T-state in complex with AMP

Components

Fructose-1,6-bisphosphatase isozyme 2

Keywords

HYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle / FBPase / T-state / AMP

Function / homology

Function and homology information

fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.845 Å

Authors

Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure.
Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A.

History

Deposition	Nov 17, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2016	Group: Database references
Revision 1.2	Aug 8, 2018	Group: Data collection / Database references / Category: pdbx_related_exp_data_set Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5et6.cif.gz	504.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5et6.ent.gz	417.7 KB	Display	PDB format
PDBx/mmJSON format	5et6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5et6_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5et6_full_validation.pdf.gz	1.9 MB	Display
Data in XML	5et6_validation.xml.gz	51.4 KB	Display
Data in CIF	5et6_validation.cif.gz	74.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/et/5et6 ftp://data.pdbj.org/pub/pdb/validation_reports/et/5et6	HTTPS FTP

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Related structure data

Related structure data	5et5C 5et7C 3ifaS 3ifc 4he0 4he1 4he2 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1fpl-1 3ifa-1 5pzq-d 5q01-2 2y5k-d 3kc1-d 2jjk-d 5q09-1 1fj9-1 5q05-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/8324764 / Data set type: diffraction image data / Metadata reference: 10.18150/8324764

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes 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: Fructose-1,6-bisphosphatase isozyme 2

C: Fructose-1,6-bisphosphatase isozyme 2

B: Fructose-1,6-bisphosphatase isozyme 2

D: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

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

1

A: Fructose-1,6-bisphosphatase isozyme 2

B: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2

B: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

defined by author&software
148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Fructose-1,6-bisphosphatase isozyme 2

D: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

C: Fructose-1,6-bisphosphatase isozyme 2

D: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

defined by author&software
148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	218.622, 234.733, 71.607
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	21
Space group name H-M	C222

#1: Protein	Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2 / Muscle FBPase Mass: 36666.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: skeletal muscle / Gene: FBP2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): C100 / References: UniProt: O00757, fructose-bisphosphatase
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.86 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium citrate tribasic / PH range: 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.82657 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 8, 2012
Radiation	Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.82657 Å / Relative weight: 1
Reflection	Resolution: 1.85→45.389 Å / Num. all: 156646 / Num. obs: 156646 / % possible obs: 99.2 % / Redundancy: 5.04 % / B_iso Wilson estimate: 34.51 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 19.43
Reflection shell	Resolution: 1.85→1.96 Å / Redundancy: 4.98 % / R_merge(I) obs: 0.693 / Mean I/σ(I) obs: 2.99 / % possible all: 97.4

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3IFA

3ifa

Resolution: 1.845→45.389 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.21 / Stereochemistry target values: ENGH & HUBER / Details: H atoms were added at riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1921	1080	0.69 %	Random selection
R_work	0.1684	-	-	-
obs	0.1686	156637	99.16 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.845→45.389 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9655	0	92	664	10411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	9964
X-RAY DIFFRACTION	f_angle_d	1.721	13489
X-RAY DIFFRACTION	f_dihedral_angle_d	15.101	3723
X-RAY DIFFRACTION	f_chiral_restr	0.102	1575
X-RAY DIFFRACTION	f_plane_restr	0.008	1691

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 (%)
1.8452-1.9292	0.3087	130	0.2706	18800	X-RAY DIFFRACTION	97
1.9292-2.0309	0.2626	135	0.2091	19400	X-RAY DIFFRACTION	100
2.0309-2.1582	0.2129	135	0.1894	19384	X-RAY DIFFRACTION	100
2.1582-2.3248	0.2072	135	0.1734	19479	X-RAY DIFFRACTION	100
2.3248-2.5587	0.1862	136	0.1775	19497	X-RAY DIFFRACTION	100
2.5587-2.9289	0.223	135	0.1838	19495	X-RAY DIFFRACTION	100
2.9289-3.6899	0.1826	136	0.1651	19609	X-RAY DIFFRACTION	99
3.6899-45.4023	0.1591	138	0.1399	19893	X-RAY DIFFRACTION	98

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	3.6146	-0.3735	0.5592	2.482	-0.4728	1.149	-0.1055	-0.0482	0.2721	0.0554	0.0264	-0.2252	0.0542	-0.012	0.0807	0.2482	-0.0014	-0.0596	0.1576	-0.0027	0.2019	14.5183	53.6879	2.6494
2	7.5932	-0.683	0.0793	3.4421	-0.8396	2.1984	-0.1151	0.2665	0.0999	-0.1571	0.0445	-0.402	-0.0688	0.0895	0.0684	0.26	0.0105	-0.0292	0.1782	0.0128	0.1547	22.2406	44.9753	-0.648
3	5.0479	-1.3891	0.6452	3.3081	-0.4058	5.6348	-0.1557	-0.5474	0.2065	0.0043	0.1197	-0.8637	0.113	0.6593	-0.0193	0.2841	-0.0094	-0.0763	0.1718	-0.0118	0.2962	26.8033	40.2569	6.3794
4	0.8674	0.1118	0.2199	1.2586	-0.2346	0.3163	-0.0846	-0.0874	-0.0293	0.0955	0.0285	-0.142	0.0103	-0.0313	0.0571	0.2868	0.0254	-0.033	0.2627	0.0094	0.0882	10.9619	29.197	8.1669
5	3.7116	1.0403	1.8322	2.035	0.4055	1.9989	-0.1124	-0.3189	0.4613	0.2789	0.0317	-0.133	-0.0005	-0.0396	0.0788	0.3616	0.0466	-0.1101	0.2175	-0.0647	0.2734	7.0463	66.3126	13.0338
6	2.0463	1.5359	1.2259	1.4751	0.3678	6.0908	-0.1535	-0.4421	0.4003	0.5105	0.1091	-0.0428	-0.1222	-0.3279	0.1336	0.4856	0.0899	-0.1703	0.3583	-0.2066	0.4088	6.535	75.0577	21.3159
7	2.4614	1.3072	0.3671	1.1431	0.9973	1.6117	0.0439	-0.5454	0.4019	0.5896	-0.0222	-0.1863	0.0651	0.2286	-0.0274	0.5322	0.0695	-0.2901	0.4072	-0.23	0.5919	14.4353	79.7294	22.8913
8	0.9964	0.0718	0.2813	1.553	0.3258	0.6808	-0.1788	-0.0775	0.7601	0.1001	0.0788	-0.164	-0.1313	0.0942	0.0183	0.3209	-0.0147	-0.2048	0.2659	-0.1139	0.7738	11.1425	90.7721	7.7402
9	2.225	-0.0816	0.3985	3.0414	-1.6102	3.3457	-0.1319	0.1235	0.2726	-0.0065	-0.1619	-0.398	-0.19	0.0688	0.2957	0.1722	-0.0037	-0.0442	0.2463	0.1072	0.3677	44.5937	14.2485	32.0171
10	3.2688	1.9588	-0.7472	7.3833	-1.0581	2.2176	-0.0012	-0.1754	0.3976	0.3366	-0.1738	-0.2951	-0.3143	0.0106	0.178	0.2605	0.0351	-0.1186	0.251	0.0552	0.328	35.6232	22.191	34.373
11	2.0846	0.5231	0.1701	0.8764	0.2385	3.6657	-0.1807	-0.024	0.8353	-0.309	0.0202	-0.1266	-0.6394	-0.2503	0.1235	0.293	0.023	-0.0908	0.2319	0.0612	0.4116	31.1089	25.9813	26.9728
12	1.7799	-0.2423	0.3264	1.3583	-0.5776	1.2577	-0.0918	-0.0197	0.1204	-0.001	0.0765	-0.0407	0.0165	-0.286	0.0165	0.245	0.0078	-0.0176	0.2868	0.0553	0.1139	20.2052	9.9028	26.5654
13	2.0116	0.6076	-0.3344	2.604	-2.016	2.8836	-0.1186	0.354	0.1878	-0.2018	-0.1334	-0.4753	0.0568	0.0909	0.2629	0.2103	0.0036	0.0449	0.391	0.1934	0.4834	57.1028	5.9907	22.3115
14	1.8238	2.3961	-1.5919	3.9303	-2.6358	7.7051	-0.0942	0.6214	-0.0427	-0.3646	-0.0101	-0.2519	0.3228	0.1579	0.135	0.2852	0.0499	0.151	0.5171	0.2332	0.5696	66.0388	4.7195	14.09
15	2.6138	1.5271	-1.6774	1.697	-0.3176	1.6202	-0.1292	0.8292	0.2292	-0.414	0.0971	-0.1979	-0.0065	-0.1672	0.3351	0.3948	0.0319	0.126	0.5872	0.3977	0.6599	70.5963	12.4256	11.8034
16	1.4112	0.3031	-0.276	0.8325	-0.273	0.7347	-0.0188	0.1933	0.143	-0.0103	-0.1901	-0.5029	-0.0766	0.0676	0.0744	0.2863	-0.0408	0.0652	0.3323	0.341	0.8386	81.5628	10.5063	27.2458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 140 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 141 through 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 336 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 88 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 89 through 140 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 141 through 167 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 168 through 334 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 9 through 88 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 89 through 140 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 141 through 167 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 168 through 334 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 9 through 88 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 89 through 140 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 141 through 167 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 168 through 334 )

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