PDB-5ucs: Class II fructose-1,6-bisphosphate aldolase E149A variant of Heli...

ID or keywords:

Entry

Database: PDB / ID: 5ucs

Title

Class II fructose-1,6-bisphosphate aldolase E149A variant of Helicobacter pylori

Components

Fructose-bisphosphate aldolase

Keywords

LYASE / Glycolysis / Metalloenzyme

Function / homology

Function and homology information

fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.408 Å

Authors

Jacques, B. / 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	Dec 22, 2016	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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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	5ucs.cif.gz	345.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ucs.ent.gz	286.1 KB	Display	PDB format
PDBx/mmJSON format	5ucs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ucs_validation.pdf.gz	439 KB	Display	wwPDB validaton report
Full document	5ucs_full_validation.pdf.gz	442.1 KB	Display
Data in XML	5ucs_validation.xml.gz	27.5 KB	Display
Data in CIF	5ucs_validation.cif.gz	42 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uc/5ucs ftp://data.pdbj.org/pub/pdb/validation_reports/uc/5ucs	HTTPS FTP

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Related structure data

Related structure data	5uckC 5ucnC 5ucpC 5uczC 5ud0C 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjeC 5vjfC 3c4uS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3n9r-3 5ud2-d 5vjf-d 3n9r-2 3c52-d 3c56-d 5ud0-d 3n9s-d 6bul-d 3n9r-1 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 (5)

Deposited unit

A: Fructose-bisphosphate aldolase

B: Fructose-bisphosphate aldolase

hetero molecules

67.7 kDa, 2 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)	39.056, 82.826, 91.095
Angle α, β, γ (deg.)	90.00, 99.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fructose-bisphosphate aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase Mass: 33742.777 Da / Num. of mol.: 2 / Mutation: E149A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: fba, HP_0176 / Production host: Escherichia coli (E. coli) / References: UniProt: P56109, fructose-bisphosphate aldolase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.15 Å³/Da / Density % sol: 42.86 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, PEG 1000, Calcium acetate, Tris-Acetic acid buffer

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.408→29.936 Å / Num. obs: 108617 / % possible obs: 65.9 % / Redundancy: 3.8 % / B_iso Wilson estimate: 14.61 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.07755 / Net I/σ(I): 8.89

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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: 3C4U

3c4u

Resolution: 1.408→29.936 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1875	4976	5.04 %
R_work	0.1638	-	-
obs	0.165	98670	89.43 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.408→29.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4484	0	4	575	5063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4636
X-RAY DIFFRACTION	f_angle_d	0.875	6245
X-RAY DIFFRACTION	f_dihedral_angle_d	20.7	1733
X-RAY DIFFRACTION	f_chiral_restr	0.073	690
X-RAY DIFFRACTION	f_plane_restr	0.006	819

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 (%)
1.4082-1.4242	0.3048	92	0.3276	2053	X-RAY DIFFRACTION	59
1.4242-1.4409	0.3847	138	0.3156	2363	X-RAY DIFFRACTION	68
1.4409-1.4585	0.3271	140	0.3078	2446	X-RAY DIFFRACTION	71
1.4585-1.4769	0.3025	132	0.2818	2588	X-RAY DIFFRACTION	74
1.4769-1.4964	0.2874	130	0.2662	2776	X-RAY DIFFRACTION	79
1.4964-1.5169	0.2986	140	0.2433	2754	X-RAY DIFFRACTION	80
1.5169-1.5385	0.2509	151	0.2357	2816	X-RAY DIFFRACTION	81
1.5385-1.5615	0.2384	164	0.2192	2965	X-RAY DIFFRACTION	84
1.5615-1.5859	0.2417	140	0.2058	2893	X-RAY DIFFRACTION	85
1.5859-1.6119	0.2136	182	0.1905	3057	X-RAY DIFFRACTION	87
1.6119-1.6397	0.2199	169	0.1911	3053	X-RAY DIFFRACTION	88
1.6397-1.6695	0.2223	144	0.1866	3105	X-RAY DIFFRACTION	89
1.6695-1.7016	0.201	169	0.1796	3141	X-RAY DIFFRACTION	90
1.7016-1.7364	0.2364	165	0.1809	3150	X-RAY DIFFRACTION	91
1.7364-1.7741	0.1897	166	0.1671	3256	X-RAY DIFFRACTION	92
1.7741-1.8154	0.1889	162	0.1724	3268	X-RAY DIFFRACTION	94
1.8154-1.8608	0.184	183	0.1667	3370	X-RAY DIFFRACTION	95
1.8608-1.9111	0.1824	180	0.1688	3284	X-RAY DIFFRACTION	96
1.9111-1.9673	0.1738	181	0.16	3380	X-RAY DIFFRACTION	97
1.9673-2.0308	0.1541	178	0.1586	3368	X-RAY DIFFRACTION	97
2.0308-2.1033	0.1812	191	0.1547	3390	X-RAY DIFFRACTION	98
2.1033-2.1875	0.1889	172	0.1463	3479	X-RAY DIFFRACTION	98
2.1875-2.287	0.1574	193	0.1438	3430	X-RAY DIFFRACTION	98
2.287-2.4076	0.196	191	0.1438	3412	X-RAY DIFFRACTION	98
2.4076-2.5583	0.1736	177	0.1473	3452	X-RAY DIFFRACTION	99
2.5583-2.7557	0.1818	196	0.1574	3492	X-RAY DIFFRACTION	99
2.7557-3.0328	0.196	185	0.1606	3477	X-RAY DIFFRACTION	99
3.0328-3.4711	0.1853	185	0.153	3485	X-RAY DIFFRACTION	100
3.4711-4.3711	0.1584	194	0.135	3506	X-RAY DIFFRACTION	99
4.3711-29.9427	0.1589	186	0.1562	3485	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	0.0262	0.0365	-0.0011	0.0705	-0.0015	0.0003	-0.0377	0.2589	-0.3155	0.0025	-0.0637	-0.0151	0.0743	-0.1948	-0.0386	0.1613	-0.042	0.0268	0.2986	-0.1279	0.2495	-7.2768	-16.1375	4.1093
2	0.1899	0.0133	0.0439	0.2343	0.148	0.3679	-0.0055	0.1153	-0.1003	0.0338	0.0043	-0.0172	0.0015	-0.0009	0.0151	0.1272	-0.0051	0.0011	0.1547	-0.0435	0.1536	2.1286	-9.2207	13.48
3	0.2137	0.0222	0.1298	0.0096	0.0092	0.0768	0.0013	0.3794	-0.2115	-0.1158	0.0346	-0.0618	0.0986	0.1687	0.0058	0.1674	-0.0006	0.0434	0.2867	-0.1416	0.2732	12.8462	-16.3094	-2.9716
4	0.1105	0.0245	-0.0795	0.0984	-0.0399	0.0883	0.0886	0.3988	-0.119	-0.034	0.0544	0.017	0.0081	-0.0632	0.0724	0.1507	-0.0052	0.0162	0.3344	-0.0912	0.1323	5.5534	-10.3108	-8.743
5	0.1309	-0.2052	-0.018	0.3623	0.0417	0.0461	0.0728	0.4198	0.0761	-0.0647	-0.0558	-0.2439	-0.1091	-0.3009	0.0082	0.1819	0.0297	0.0011	0.351	-0.0557	0.1351	-0.0868	-1.3948	-5.7858
6	0.0829	0.0116	0.0382	0.0561	0.0546	0.0533	-0.0461	0.1728	0.0919	-0.1197	-0.0491	0.0317	-0.1529	0.0243	-0.1546	0.1653	0.0602	-0.0678	-0.0014	0.1146	0.0879	-3.3857	15.8385	11.8325
7	0.0206	-0.0046	0.022	0.1379	-0.0187	0.0342	0.0696	0.255	0.028	-0.0091	-0.0474	-0.0646	-0.1329	-0.2904	0.005	0.1971	0.0475	-0.0093	0.3472	-0.0408	0.1346	-7.3204	0.4423	-0.0812
8	0.3441	-0.103	-0.1179	0.0781	0.2327	0.1075	0.0174	0.0777	0.0705	0.0083	-0.0384	0.0165	-0.107	-0.1579	0.0049	0.1683	0.0118	-0.0162	0.1211	-0.0041	0.136	-5.8296	5.6204	20.8302
9	0.0207	0.0189	-0.0148	0.0393	-0.0246	0.0147	-0.0414	-0.0775	-0.1977	0.0055	0.0823	-0.0374	0.1392	0.1642	0.0001	0.1189	0.0184	-0.0028	0.1505	0.0252	0.1333	14.4025	-15.5095	48.8746
10	0.1252	0.0925	0.0171	0.2348	-0.176	0.2876	0.0287	-0.065	-0.0276	-0.013	0.0011	0.0277	-0.0221	0.0165	0.0055	0.1092	0.003	0.001	0.1034	0.017	0.1265	5.876	-9.0081	37.8007
11	0.2367	-0.0004	0.0541	0.3586	-0.1023	0.1481	0.0233	-0.3057	-0.1111	0.0405	0.0534	0.1404	-0.0219	-0.1457	0.0341	0.1298	0.0156	0.0222	0.2274	0.0399	0.1437	-2.3953	-11.7539	57.2055
12	0.1963	0.0686	0.035	0.0226	0.0236	0.1409	0.0554	-0.3349	0.0964	0.0919	-0.0286	0.1696	-0.1564	0.03	0	0.2067	-0.0113	0.018	0.2208	-0.04	0.1615	7.044	-0.4135	58.5406
13	0.1102	-0.0351	0.0974	0.0157	-0.0339	0.1801	0.0061	-0.1921	0.271	0.121	-0.1253	-0.1319	-0.14	-0.1194	-0.0072	0.1698	-0.0868	-0.0453	0.0166	-0.0956	0.2531	10.1579	16.0401	40.6884
14	0.3912	0.0631	-0.0235	0.2416	-0.1283	0.0479	0.0097	-0.0541	0.0849	-0.0177	-0.009	-0.0076	-0.0875	0.1319	0.0116	0.1791	-0.0111	-0.0064	0.1154	-0.0076	0.154	12.9131	4.5415	37.164

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 109 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 110 through 127 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 167 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 216 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 217 through 237 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 238 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 307 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 15 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 16 through 96 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 97 through 167 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 168 through 216 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 217 through 237 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 238 through 307 )

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