PDB-5ky6: Human muscle fructose-1,6-bisphosphate aldolase

ID or keywords:

Entry

Database: PDB / ID: 5ky6

Title

Human muscle fructose-1,6-bisphosphate aldolase

Components

Fructose-bisphosphate aldolase A

Keywords

LYASE / aldolase / muscle / glycolysis / glyconeogenesis

Function / homology

Function and homology information

fructose binding / fructose 1,6-bisphosphate metabolic process / sperm head / ATP biosynthetic process / binding of sperm to zona pellucida / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose metabolic process / Gluconeogenesis / muscle cell cellular homeostasis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.941 Å

Authors

Wisniewski, J. / Barciszewski, J. / Jaskolski, M. / Rakus, D.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of human muscle aldolase
Authors: Wisniewski, J. / Barciszewski, J. / Jaskolski, M. / Rakus, D.

History

Deposition	Jul 21, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ky6.cif.gz	723 KB	Display	PDBx/mmCIF format
PDB format	pdb5ky6.ent.gz	615.8 KB	Display	PDB format
PDBx/mmJSON format	5ky6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ky/5ky6 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5ky6	HTTPS FTP

-
Related structure data

Related structure data	2aldS S: Starting model for refinement
Similar structure data	5tle-d 5tlz-d 2quv-d 3tu9-d 7ka3-d 5tkl-1 1epx-d 6rng-1 1qo5-3 2qap-d 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/repod.1494374 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (8) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Fructose-bisphosphate aldolase A

B: Fructose-bisphosphate aldolase A

C: Fructose-bisphosphate aldolase A

D: Fructose-bisphosphate aldolase A

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	84.511, 57.253, 164.016
Angle α, β, γ (deg.)	90.00, 102.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fructose-bisphosphate aldolase A / Lung cancer antigen NY-LU-1 / Muscle-type aldolase Mass: 39338.777 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Gaps in the sequence indicate residues that were not modelled because of poor electron density Source: (gene. exp.) Homo sapiens (human) / Tissue: muscle / Gene: ALDOA, ALDA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P04075, fructose-bisphosphate aldolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Fructose-bisphosphate aldolase A / Lung cancer antigen NY-LU-1 / Muscle-type aldolase

Mass: 39338.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Gaps in the sequence indicate residues that were not modelled because of poor electron density
Source: (gene. exp.)

Homo sapiens (human) / Tissue: muscle / Gene: ALDOA, ALDA / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: P04075, fructose-bisphosphate aldolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.14 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium citrate tribasic

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2012
Radiation	Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.94→46.72 Å / Num. obs: 112653 / % possible obs: 99 % / Redundancy: 5.68 % / R_merge(I) obs: 0.166 / Net I/σ(I): 10.01
Reflection shell	Resolution: 1.94→2.06 Å / Redundancy: 5.34 % / R_merge(I) obs: 0.721 / Mean I/σ(I) obs: 2.85 / % possible all: 94.4

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ALD

2ald

Resolution: 1.941→46.721 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2227	1001	89 %	Random selection
R_work	0.1864	-	-	-
obs	0.1867	112632	99.02 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.941→46.721 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10080	0	0	562	10642

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	10295
X-RAY DIFFRACTION	f_angle_d	0.971	13959
X-RAY DIFFRACTION	f_dihedral_angle_d	12.468	6273
X-RAY DIFFRACTION	f_chiral_restr	0.054	1594
X-RAY DIFFRACTION	f_plane_restr	0.007	1811

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 (%)
1.9411-2.0435	0.3301	135	0.265	15049	X-RAY DIFFRACTION	94
2.0435-2.1715	0.279	143	0.2145	15953	X-RAY DIFFRACTION	100
2.1715-2.3391	0.2569	143	0.2015	15969	X-RAY DIFFRACTION	100
2.3391-2.5745	0.2318	144	0.1893	16038	X-RAY DIFFRACTION	100
2.5745-2.947	0.2495	144	0.1825	16068	X-RAY DIFFRACTION	100
2.947-3.7127	0.1847	145	0.1723	16168	X-RAY DIFFRACTION	100
3.7127-46.735	0.184	147	0.1637	16386	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	0.9837	-0.3516	-0.148	0.7657	0.1297	0.5431	-0.0501	0.0006	-0.0583	0.0134	0.1243	-0.1269	-0.0104	0.3575	-0.0437	0.1192	-0.0144	0.0076	0.2392	-0.0499	0.1478	17.2022	58.0935	22.2558
2	0.3572	0.0714	-0.2378	0.3725	-0.0583	0.6648	-0.0184	0.0734	-0.0009	0.0329	0.119	-0.0459	0.1156	0.4216	0.0316	0.0894	-0.0222	0.0127	0.2629	-0.0419	0.1243	15.3142	54.4862	31.5577
3	0.2606	0.0897	0.0212	0.5087	0.1405	0.382	-0.0321	0.0207	-0.0618	-0.1086	0.0439	-0.0709	0.0824	0.1301	-0.0167	0.1551	-0.0268	0.0035	0.0318	-0.0123	0.1182	-0.1642	50.905	27.7627
4	0.9793	0.006	-0.2621	0.4882	0.038	0.5352	-0.0464	0.1288	-0.1098	-0.0678	0.1439	-0.1583	0.1684	0.2131	-0.0588	0.1771	-0.0136	0.0062	0.1411	-0.0669	0.1274	7.3897	47.9689	12.721
5	0.662	0.3037	-0.3543	0.6328	-0.2929	0.2307	-0.0034	0.0118	0.0343	-0.0642	0.126	0.1317	-0.0939	-0.2278	-0.0692	0.1508	0.0074	0.008	0.2379	0.0863	0.1595	-35.252	57.5151	54.8622
6	0.2568	0.0485	-0.1121	0.0261	-0.0672	0.3017	-0.0055	-0.042	-0.072	-0.0242	0.1338	0.1379	0.1042	-0.4429	0.083	-0.051	-0.0881	0.0359	0.4986	0.184	0.211	-42.2658	49.3413	49.11
7	0.4224	-0.1898	-0.0747	0.5875	-0.1603	0.4688	0.0068	0.0233	-0.0523	-0.0275	0.1064	0.0974	0.1859	-0.2392	-0.0552	0.1567	-0.0243	-0.0305	0.0601	0.0577	0.108	-23.7994	47.3794	48.7698
8	0.4251	0.0839	-0.2982	0.5318	-0.0502	0.4176	-0.0428	-0.0039	-0.1104	0.0505	0.0377	0.0777	0.1792	-0.179	-0.0518	0.1204	-0.0499	-0.0354	0.077	0.0842	0.0816	-27.4508	40.8767	60.6884
9	1.2544	-0.1375	0.0263	0.424	-0.0072	0.4748	0.0573	-0.0676	-0.1993	0.0296	0.0583	-0.0401	0.1138	-0.1568	-0.0227	0.2277	-0.0685	-0.0158	0.1989	0.0948	0.1794	-32.3649	36.4061	65.7063
10	0.4032	-0.221	0.3325	0.7733	-0.4415	0.6314	-0.0091	0.1367	0.0241	0.0041	0.1125	0.1297	0.0663	-0.1643	-0.0266	0.1707	-0.0691	0.0091	0.2789	0.1022	0.196	-26.4324	56.3673	15.3485
11	0.366	0.0307	-0.0811	0.2084	-0.1309	0.6748	0.0939	0.2195	0.1774	0.0227	0.1926	0.1655	-0.178	-0.5277	0.1868	0.0719	-0.0096	-0.0641	0.3216	0.1567	0.1476	-29.5331	64.6152	21.1656
12	0.5399	0.4085	0.1556	0.9245	-0.0043	0.48	0.0439	0.1018	0.161	-0.0747	0.0725	0.115	-0.1491	-0.0985	-0.0527	0.1872	-0.0044	0.033	0.1133	0.0577	0.1569	-17.2092	70.4979	21.4213
13	0.2897	-0.0911	0.0671	0.2575	-0.1753	0.389	0.0672	0.1871	0.1959	-0.0279	0.1537	0.0884	-0.2024	-0.2465	0.1988	0.1802	0.013	0.0141	0.1463	0.2035	0.1142	-17.7828	74.3827	11.08
14	0.6465	0.1103	0.082	0.4626	0.0654	0.6195	-0.0335	-0.1327	0.0415	0.0356	0.1065	-0.1358	0.0581	0.3779	-0.0355	0.1118	0.008	-0.0094	0.2319	-0.0451	0.1379	9.9393	55.1384	68.2577
15	0.4806	0.0415	0.1843	0.4936	-0.2339	0.9942	0.0224	-0.0442	0.055	-0.0377	0.0597	-0.0483	-0.2035	0.2006	0.0053	0.0868	-0.0157	0.0098	0.0996	-0.0142	0.0988	5.2725	61.0854	51.5459
16	0.2218	-0.0984	-0.0519	0.5677	0.1066	0.2946	0.0596	-0.0561	0.0872	0.0377	0.0076	-0.0494	-0.1339	0.1214	-0.0175	0.1512	0.0009	0.0115	0.048	-0.0037	0.1336	-6.191	62.6448	54.9938
17	0.6548	0.0221	0.3232	0.5626	0.0136	0.7807	0.0325	-0.125	0.117	0.06	0.1017	-0.0865	-0.1837	0.1309	-0.0428	0.1561	-0.0097	0.0178	0.0967	-0.0463	0.1204	-5.3487	65.6456	71.9794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 159 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 160 through 244 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 245 through 343 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 51 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 52 through 159 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 160 through 244 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 245 through 319 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 320 through 363 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 51 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 52 through 218 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 219 through 244 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 245 through 363 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 107 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 108 through 159 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 160 through 244 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 245 through 343 )

-
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

-
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

-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

-
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