PDB-5vje: Class II fructose-1,6-bisphosphate aldolase of Escherichia coli w...

ID or keywords:

Entry

Database: PDB / ID: 5vje

Title

Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with D-glucitol 1,6-bisphosphate

Components

Fructose-bisphosphate aldolase class 2

Keywords

LYASE /

Glycolysis

Function / homology

Function and homology information

fructose-bisphosphate aldolase /

fructose-bisphosphate aldolase activity /

gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Coincon, M. / Sygusch, J.

Funding support

Canada, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.
Authors: Jacques, B. / Coincon, M. / Sygusch, J.

History

Deposition	Apr 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vje.cif.gz	411.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5vje.ent.gz	340.5 KB	Display	PDB format
PDBx/mmJSON format	5vje.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/vj/5vje ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vje	HTTPS FTP

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Related structure data

Related structure data	5uckC 5ucnC 5ucpC 5ucsC 5uczC 5ud0C 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjfC 1b57S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5vjd-d 1gyn-1 5gk7-d 1b57-d 5gk3-d 1lox-d 6hzh-d 3sni-d 1k7f-d 6mq9-5 Search similar-shape structures by Omokage search (details) 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 (7)

Deposited unit

A: Fructose-bisphosphate aldolase class 2

B: Fructose-bisphosphate aldolase class 2

hetero molecules

78.9 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)	57.250, 71.869, 88.983
Angle α, β, γ (deg.)	90.00, 108.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fructose-bisphosphate aldolase class 2 / FBPA / Fructose-1 / 6-bisphosphate aldolase / Fructose-bisphosphate aldolase class II Mass: 39059.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB71, fructose-bisphosphate aldolase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-GOS / D-Glucitol-1,6-bisphosphate / 1,6-di-O-phosphono-D-glucitol Mass: 342.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₆O₁₂P₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1077 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 4000, MgCl2, Hepes buffer

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.99 Å
Detector	Type: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 1, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 1.65→29.011 Å / Num. obs: 81148 / % possible obs: 98.3 % / Redundancy: 5.7 % / B_iso Wilson estimate: 16.1 Å² / R_sym value: 0.09 / Net I/σ(I): 28.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1B57

1b57

Resolution: 1.65→29.011 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.96

	R_factor	Num. reflection	% reflection
R_free	0.1642	6493	8 %
R_work	0.1377	-	-
obs	0.1398	81148	98.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.65→29.011 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5252	0	44	1077	6373

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5430
X-RAY DIFFRACTION	f_angle_d	0.824	7372
X-RAY DIFFRACTION	f_dihedral_angle_d	14.002	3220
X-RAY DIFFRACTION	f_chiral_restr	0.05	819
X-RAY DIFFRACTION	f_plane_restr	0.006	950

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 (%)
1.6499-1.6687	0.2903	193	0.2426	2104	X-RAY DIFFRACTION	84
1.6687-1.6883	0.2301	198	0.2248	2225	X-RAY DIFFRACTION	89
1.6883-1.7089	0.2544	198	0.2191	2314	X-RAY DIFFRACTION	92
1.7089-1.7305	0.23	206	0.2049	2393	X-RAY DIFFRACTION	95
1.7305-1.7533	0.2336	209	0.1972	2437	X-RAY DIFFRACTION	97
1.7533-1.7773	0.2132	218	0.1866	2521	X-RAY DIFFRACTION	100
1.7773-1.8027	0.2024	218	0.1691	2529	X-RAY DIFFRACTION	100
1.8027-1.8296	0.1955	214	0.162	2483	X-RAY DIFFRACTION	100
1.8296-1.8582	0.1852	222	0.1539	2521	X-RAY DIFFRACTION	100
1.8582-1.8886	0.1779	222	0.1479	2510	X-RAY DIFFRACTION	100
1.8886-1.9212	0.1706	218	0.1461	2502	X-RAY DIFFRACTION	100
1.9212-1.9561	0.2013	213	0.1434	2542	X-RAY DIFFRACTION	100
1.9561-1.9937	0.1857	221	0.1355	2524	X-RAY DIFFRACTION	100
1.9937-2.0344	0.159	219	0.141	2532	X-RAY DIFFRACTION	100
2.0344-2.0786	0.1799	214	0.1382	2508	X-RAY DIFFRACTION	100
2.0786-2.127	0.155	221	0.1288	2523	X-RAY DIFFRACTION	100
2.127-2.1801	0.1495	219	0.1245	2524	X-RAY DIFFRACTION	100
2.1801-2.2391	0.1395	220	0.1231	2522	X-RAY DIFFRACTION	100
2.2391-2.3049	0.1459	223	0.1152	2507	X-RAY DIFFRACTION	100
2.3049-2.3793	0.1339	230	0.1162	2530	X-RAY DIFFRACTION	100
2.3793-2.4643	0.1582	217	0.1179	2505	X-RAY DIFFRACTION	100
2.4643-2.5629	0.1703	217	0.1213	2533	X-RAY DIFFRACTION	100
2.5629-2.6795	0.1603	225	0.1286	2520	X-RAY DIFFRACTION	100
2.6795-2.8206	0.1596	215	0.1328	2533	X-RAY DIFFRACTION	100
2.8206-2.9972	0.1785	217	0.1334	2547	X-RAY DIFFRACTION	100
2.9972-3.2283	0.1679	215	0.1357	2525	X-RAY DIFFRACTION	100
3.2283-3.5527	0.1411	222	0.131	2563	X-RAY DIFFRACTION	100
3.5527-4.0655	0.1473	220	0.1247	2550	X-RAY DIFFRACTION	100
4.0655-5.1176	0.1452	222	0.1131	2552	X-RAY DIFFRACTION	100
5.1176-29.0156	0.1553	227	0.165	2576	X-RAY DIFFRACTION	99

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	0.1244	0.0051	0.1159	0.3109	0.0004	0.2627	0.0397	0.0357	-0.033	0.0692	-0.0576	-0.0916	-0.0333	0.0955	-0.0112	0.0961	-0.0042	-0.0224	0.1431	0.0236	0.1626	31.2948	-12.7065	54.7868
2	0.755	0.6495	-0.1184	0.4411	-0.1718	0.2681	0.1157	-0.0832	0.0363	0.1407	-0.1114	0.0317	-0.0389	0.0248	0.0067	0.1339	-0.0206	0.0001	0.1167	-0.0056	0.1104	17.4037	-12.4478	65.4209
3	0.3938	0.2034	-0.1668	0.1048	-0.0911	0.4154	0.1544	-0.1624	0.0771	0.1514	-0.1147	-0.0187	-0.1583	0.1098	0.054	0.2102	-0.0808	-0.0034	0.1718	-0.0246	0.1655	29.7138	2.3247	67.0819
4	0.1532	0.1686	-0.2831	0.4151	-0.0313	0.4264	0.1316	0.0839	0.2096	0.0186	-0.0304	0.1441	-0.1238	-0.0543	0.0001	0.1316	-0.0071	0.0091	0.1439	0.0479	0.2055	27.7748	4.4146	50.2445
5	0.2316	-0.0916	0.1246	0.1393	0.1289	0.1356	-0.001	0.1102	-0.0552	-0.0125	-0.004	-0.0294	-0.0049	-0.0179	-0.0003	0.1041	-0.0008	-0.005	0.1545	0.0098	0.1204	-5.3977	-19.1217	46.2583
6	0.1522	-0.0005	0.1071	0.0223	-0.0586	0.0518	-0.0322	0.1936	-0.0224	-0.0294	0.0335	-0.0392	0.0207	-0.0301	-0	0.1096	-0.0102	0.0155	0.1624	0.0007	0.1349	15.1134	-15.0308	46.6896
7	0.424	0.1608	-0.1913	0.6689	-0.4309	0.4812	0.0381	-0.0556	-0.0258	0.0067	-0.0426	-0.0691	0.0084	0.0179	-0.0003	0.124	-0.0071	-0.0083	0.0979	0.0057	0.0946	4.0609	-30.4464	71.0945
8	0.0884	0.0432	-0.1065	0.1683	-0.0694	0.1471	-0.042	-0.1003	-0.1421	-0.1286	-0.0694	-0.097	0.0934	-0.0204	-0.004	0.2086	-0.0004	0.0015	0.1069	0.0125	0.1672	1.689	-47.2502	70.3397
9	0.6763	0.2062	-0.4512	0.6053	-0.0808	0.3799	0.0024	0.087	-0.0303	-0.131	-0.0046	0.0797	0.1075	-0.1733	-0.0198	0.1737	-0.0457	-0.0263	0.164	0.0115	0.1161	-12.0596	-42.4374	71.8159
10	0.505	-0.1396	0.2029	0.1837	0.0813	0.2214	0.1777	0.2039	0.2448	0.1134	-0.1965	0.1571	-0.0721	-0.0228	-0.0352	0.103	0.0564	0.0096	0.1327	0.0968	0.1708	-4.0549	-6.2891	50.4687
11	0.1462	-0.0595	0.1135	0.0706	-0.1578	0.1017	0.053	-0.0384	0.0828	0.091	0.0129	0.057	-0.1053	-0.0585	-0	0.1445	0.0068	0.0251	0.124	0.0065	0.1222	-8.2535	-17.844	67.541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 133 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 134 through 220 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 221 through 288 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 289 through 329 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 330 through 358 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 149 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 150 through 198 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 199 through 288 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 289 through 329 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 330 through 358 )

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