PDB-5ud0: Class II fructose-1,6-bisphosphate aldolase E149A variant of Heli...

ID or keywords:

Entry

Database: PDB / ID: 5ud0

Title

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

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: 1.647 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 23, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_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	5ud0.cif.gz	339.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ud0.ent.gz	279 KB	Display	PDB format
PDBx/mmJSON format	5ud0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ud0_validation.pdf.gz	468.2 KB	Display	wwPDB validaton report
Full document	5ud0_full_validation.pdf.gz	472.5 KB	Display
Data in XML	5ud0_validation.xml.gz	27.1 KB	Display
Data in CIF	5ud0_validation.cif.gz	39.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ud/5ud0 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/5ud0	HTTPS FTP

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Related structure data

Related structure data	5uckC 5ucnC 5ucpC 5ucsC 5uczC 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjeC 5vjfC 3c4uS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3n9r-3 3n9s-d 2yfd-d 2nxo-1 3n9r-1 5ucs-d 4mpd-1 6fqi-d 5ud3-d 3bfv-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

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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

B: Fructose-bisphosphate aldolase

hetero molecules

68.1 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)	39.258, 85.386, 91.082
Angle α, β, γ (deg.)	90.00, 100.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#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

#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

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Non-polymers , 6 types, 467 molecules

#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.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#6: Chemical	ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.23 Å³/Da / Density % sol: 44.75 %
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: 08B1-1 / Wavelength: 1.03322 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03322 Å / Relative weight: 1
Reflection	Resolution: 1.647→29.881 Å / Num. obs: 68950 / % possible obs: 90.22 % / Redundancy: 3.1 % / CC_1/2: 0.993 / R_merge(I) obs: 0.08529 / Net I/σ(I): 8.44

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2481)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3C4U

3c4u

Resolution: 1.647→29.881 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.81

	R_factor	Num. reflection	% reflection
R_free	0.2226	3274	5.08 %
R_work	0.178	-	-
obs	0.1802	64399	90.24 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.647→29.881 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4429	0	26	459	4914

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4532
X-RAY DIFFRACTION	f_angle_d	0.919	6091
X-RAY DIFFRACTION	f_dihedral_angle_d	13.944	2748
X-RAY DIFFRACTION	f_chiral_restr	0.051	678
X-RAY DIFFRACTION	f_plane_restr	0.006	788

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 (%)
1.6475-1.6721	0.3703	94	0.3069	1698	X-RAY DIFFRACTION	58
1.6721-1.6982	0.381	114	0.2851	2169	X-RAY DIFFRACTION	74
1.6982-1.726	0.3069	117	0.2655	2259	X-RAY DIFFRACTION	77
1.726-1.7558	0.2802	137	0.2569	2367	X-RAY DIFFRACTION	81
1.7558-1.7877	0.3026	102	0.228	2440	X-RAY DIFFRACTION	81
1.7877-1.8221	0.2656	137	0.2154	2415	X-RAY DIFFRACTION	84
1.8221-1.8593	0.2734	127	0.2105	2531	X-RAY DIFFRACTION	86
1.8593-1.8997	0.2081	149	0.1974	2530	X-RAY DIFFRACTION	87
1.8997-1.9439	0.2828	133	0.1932	2642	X-RAY DIFFRACTION	90
1.9439-1.9925	0.2351	151	0.1924	2702	X-RAY DIFFRACTION	92
1.9925-2.0464	0.2396	151	0.1844	2707	X-RAY DIFFRACTION	93
2.0464-2.1066	0.2346	146	0.1814	2727	X-RAY DIFFRACTION	93
2.1066-2.1745	0.2332	147	0.1706	2786	X-RAY DIFFRACTION	94
2.1745-2.2522	0.2298	147	0.1674	2807	X-RAY DIFFRACTION	95
2.2522-2.3424	0.2363	150	0.1614	2844	X-RAY DIFFRACTION	96
2.3424-2.4489	0.2195	163	0.158	2895	X-RAY DIFFRACTION	98
2.4489-2.578	0.208	152	0.1664	2894	X-RAY DIFFRACTION	99
2.578-2.7394	0.2292	160	0.1738	2938	X-RAY DIFFRACTION	100
2.7394-2.9507	0.2319	161	0.1711	2926	X-RAY DIFFRACTION	99
2.9507-3.2474	0.2226	155	0.176	2957	X-RAY DIFFRACTION	100
3.2474-3.7165	0.2102	151	0.1648	2946	X-RAY DIFFRACTION	99
3.7165-4.6795	0.1669	164	0.1496	2952	X-RAY DIFFRACTION	100
4.6795-29.8856	0.2078	166	0.1834	2993	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	0.0034	0.0008	-0.0008	0.0014	-0.0021	0.0022	-0.0077	-0.0086	-0.0432	-0.0476	0.0251	0.0638	0.0283	0.0024	-0	0.2259	-0.0085	-0.0034	0.3574	0.1231	0.2014	13.2227	-17.8943	49.0499
2	0.0174	-0.0195	0.0171	0.4993	0.1314	0.1565	-0.0452	-0.3297	-0.1011	-0.0772	0.0435	-0.04	-0.0297	-0.036	0.0547	0.106	0.0116	0.007	0.1955	0.0545	0.1414	4.1133	-11.2828	39.4333
3	0.0103	0.0143	-0.0299	0.0095	-0.0209	0.0457	-0.0033	-0.2346	0.0099	0.0876	0.0458	0.0723	-0.0014	-0.0875	0.0375	0.1098	0.0126	0.0832	0.7086	0.1714	0.1092	-2.605	-14.6332	59.1964
4	0.2038	0.0571	-0.0284	0.0179	0.0041	0.0441	0.0028	-0.1422	0.0849	0.0632	-0.0093	0.0468	-0.0724	-0.0329	-0.0189	0.1741	0.038	0.0126	0.5841	0.0513	0.1407	7.5858	-4.5921	58.6225
5	0.1879	0.0165	-0.0678	0.0061	0.001	0.0276	-0.0364	-0.3291	0.0349	-0.0307	0.0242	-0.007	-0.157	0.098	-0.0146	0.2532	0.0225	-0.0656	0.2896	-0.0832	0.1596	11.4327	6.5558	46.4161
6	0.4689	0.0096	-0.2223	0.0234	0.0049	0.119	-0.1033	-0.2245	0.0881	-0.1875	-0.0132	0.0244	-0.1947	0.1279	-0.1812	0.2352	-0.0545	-0.0586	0.0611	-0.0568	0.1171	11.9571	3.2656	31.6331
7	0.0023	-0.0014	0.0027	0.0062	0.0057	0.0066	-0.0007	0.0387	-0.0727	0.0235	-0.0218	-0.0158	0.0359	-0.036	-0.0062	0.1164	-0.0334	0.0158	0.1827	-0.0704	0.2031	-7.5311	-19.4474	4.4415
8	0.0948	0.0024	0.0602	0.1122	-0.0599	0.1047	-0.0279	0.0838	-0.1007	0.0775	0.0137	0.011	-0.0474	0.0059	0.0405	0.1004	-0.0087	0.0172	0.0688	-0.0216	0.1442	1.8283	-12.1753	13.6349
9	0.0076	-0.0037	-0.0059	0.0038	0.0078	0.0159	0.0506	0.1153	-0.0414	-0.0367	-0.0063	-0.0137	-0.005	0.0574	0.0265	0.1458	-0.0111	0.0628	0.3246	-0.1013	0.2426	12.5036	-19.8881	-2.5637
10	0.0632	-0.0468	0.0153	0.0384	-0.0166	0.0104	0.042	0.1376	-0.0369	-0.0959	0.0308	-0.0246	0.0245	0.0138	0.0216	0.1678	-0.0431	0.0514	0.2265	-0.0964	0.1819	6.0376	-13.347	-8.2393
11	0.0113	-0.0076	0.0059	0.0062	-0.007	0.0047	-0.0289	0.0662	0.0606	0.0776	-0.001	-0.0332	-0.1459	0.0302	-0.0014	0.2028	-0.0495	-0.0169	0.2017	-0.0514	0.1621	2.5683	-5.1492	-1.3419
12	0.0209	-0.0113	0.0085	0.0483	0.0155	0.0134	-0.0553	0.127	0.1007	-0.066	-0.0241	-0.0832	-0.0544	-0.0219	-0.0217	0.2195	-0.0112	-0.0074	0.2275	-0.044	0.1366	-3.1968	-2.9465	-6.5017
13	0.5355	0.0315	-0.1576	0.0749	0.0431	0.0956	-0.0728	0.2217	0.0433	0.0886	-0.0053	-0.0412	-0.2141	-0.072	-0.0498	0.2469	0.0305	-0.0648	0.087	0.0268	0.1496	-5.8425	5.2421	5.5037
14	0.0539	-0.0222	-0.0206	0.0731	-0.0389	0.1277	-0.0729	-0.0062	0.0342	0.1546	0.021	0.0258	-0.115	-0.1262	-0.0244	0.2222	0.042	-0.0297	0.0426	-0.0251	0.1546	-6.2535	2.8838	20.5648

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 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 216 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 217 through 255 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 256 through 307 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 15 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 16 through 109 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 110 through 127 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 128 through 167 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 168 through 184 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 185 through 216 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 217 through 255 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 256 through 307 )

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