PDB-5ucp: Class II fructose-1,6-bisphosphate aldolase E142A variant of Heli...

ID or keywords:

Entry

Database: PDB / ID: 5ucp

Title

Class II fructose-1,6-bisphosphate aldolase E142A variant of Helicobacter pylori with FBP and 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: 1.444 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.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	5ucp.cif.gz	349.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5ucp.ent.gz	289.7 KB	Display	PDB format
PDBx/mmJSON format	5ucp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ucp_validation.pdf.gz	795.6 KB	Display	wwPDB validaton report
Full document	5ucp_full_validation.pdf.gz	800.5 KB	Display
Data in XML	5ucp_validation.xml.gz	28.5 KB	Display
Data in CIF	5ucp_validation.cif.gz	42.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uc/5ucp ftp://data.pdbj.org/pub/pdb/validation_reports/uc/5ucp	HTTPS FTP

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Related structure data

Related structure data	5uckC 5ucnC 5ucsC 5uczC 5ud0C 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjeC 5vjfC 3c4uS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ud2-d 3n9r-2 5ud4-d 3n9r-4 5vjf-d 5uck-d 3n9r-3 1x7d-d 5ucz-d 5ucs-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

68.6 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)	39.476, 64.633, 62.845
Angle α, β, γ (deg.)	82.15, 74.39, 75.78
Int Tables number	1
Space group name H-M	P1

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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: E142A 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: E142A
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, 543 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.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-P6F / 1,6-di-O-phosphono-D-fructose Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂
#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.: 532 / 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: 2.21 Å³/Da / Density % sol: 44.39 %
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: 1.444→29.213 Å / Num. obs: 95440 / % possible obs: 82.23 % / Redundancy: 2.1 % / B_iso Wilson estimate: 12.69 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.06679 / Net I/σ(I): 7.41

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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: 1.444→29.213 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 23.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1957	4030	4.72 %
R_work	0.1616	-	-
obs	0.1632	85328	82.15 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.444→29.213 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4525	0	48	532	5105

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4775
X-RAY DIFFRACTION	f_angle_d	0.832	6443
X-RAY DIFFRACTION	f_dihedral_angle_d	17.633	1784
X-RAY DIFFRACTION	f_chiral_restr	0.062	706
X-RAY DIFFRACTION	f_plane_restr	0.005	839

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 (%)
1.4437-1.4607	0.4392	59	0.3325	1330	X-RAY DIFFRACTION	38
1.4607-1.4785	0.2922	81	0.3182	1733	X-RAY DIFFRACTION	52
1.4785-1.4973	0.2637	93	0.2979	1862	X-RAY DIFFRACTION	54
1.4973-1.517	0.3345	116	0.2895	1986	X-RAY DIFFRACTION	59
1.517-1.5377	0.3398	97	0.2892	2214	X-RAY DIFFRACTION	65
1.5377-1.5597	0.2966	98	0.266	2324	X-RAY DIFFRACTION	67
1.5597-1.583	0.3155	124	0.2591	2384	X-RAY DIFFRACTION	70
1.583-1.6077	0.2527	122	0.2504	2556	X-RAY DIFFRACTION	75
1.6077-1.6341	0.2872	130	0.2503	2570	X-RAY DIFFRACTION	75
1.6341-1.6622	0.2697	127	0.2383	2661	X-RAY DIFFRACTION	78
1.6622-1.6925	0.2554	129	0.2315	2762	X-RAY DIFFRACTION	80
1.6925-1.725	0.2624	150	0.2252	2724	X-RAY DIFFRACTION	81
1.725-1.7602	0.2284	152	0.2124	2845	X-RAY DIFFRACTION	83
1.7602-1.7985	0.2622	127	0.1953	2895	X-RAY DIFFRACTION	84
1.7985-1.8403	0.2331	150	0.1863	2905	X-RAY DIFFRACTION	86
1.8403-1.8863	0.2275	143	0.1781	3059	X-RAY DIFFRACTION	89
1.8863-1.9373	0.2036	160	0.166	3051	X-RAY DIFFRACTION	91
1.9373-1.9943	0.171	163	0.1564	3181	X-RAY DIFFRACTION	92
1.9943-2.0587	0.1831	153	0.1564	3162	X-RAY DIFFRACTION	93
2.0587-2.1322	0.1728	159	0.1515	3203	X-RAY DIFFRACTION	95
2.1322-2.2176	0.1896	166	0.1438	3287	X-RAY DIFFRACTION	95
2.2176-2.3185	0.1762	157	0.1421	3281	X-RAY DIFFRACTION	95
2.3185-2.4406	0.1782	169	0.1463	3239	X-RAY DIFFRACTION	97
2.4406-2.5935	0.1667	160	0.15	3327	X-RAY DIFFRACTION	97
2.5935-2.7936	0.226	167	0.1531	3327	X-RAY DIFFRACTION	97
2.7936-3.0744	0.2004	172	0.1507	3325	X-RAY DIFFRACTION	98
3.0744-3.5187	0.1504	171	0.1384	3342	X-RAY DIFFRACTION	99
3.5187-4.4306	0.1501	167	0.1145	3385	X-RAY DIFFRACTION	99
4.4306-29.2188	0.1731	168	0.1377	3378	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	0.0008	0.0014	-0.0001	0.0018	-0.0029	0.0041	0.0132	-0.0567	0.016	-0.0008	0.0102	-0.0261	0.0457	0.0167	0	0.0985	0.0152	-0.011	0.1857	-0.0269	0.1377	1.6946	18.1407	-15.2402
2	0.0379	0.0265	0.0379	0.0651	0.0322	0.0893	-0.0243	-0.0374	0.0475	-0.0532	0.0189	0.0208	0.0027	-0.0107	-0.0074	0.0669	0.0121	-0.0043	0.1085	-0.0034	0.0803	-7.7155	16.0131	-26.6595
3	0.0078	0.0008	0.0003	0.0034	-0.0019	0.0086	0.0405	-0.1096	0.0611	0.0346	-0.0273	0.0537	-0.0205	-0.0749	0.0014	0.0843	0.0069	0.0103	0.1902	-0.0579	0.152	-18.1917	23.0782	-10.1862
4	0.0183	0.0035	0.0069	0.0101	-0.002	0.018	0.0417	-0.0784	0.0977	0.0357	0.0053	-0.0116	-0.0325	-0.0641	0.0071	0.1156	0.0277	0.0105	0.1809	-0.0519	0.1578	-11.6611	32.0016	-11.7673
5	0.0305	0.0297	-0.0101	0.0348	-0.0195	0.0225	0.0679	0.0073	0.1747	-0.0647	0.1199	-0.0198	-0.1199	-0.0582	0.0243	0.1661	0.0084	0.035	0.168	-0.0332	0.1928	-4.763	35.0955	-21.2995
6	0.0138	0.0098	-0.0072	0.0061	-0.0054	0.0045	-0.0047	-0.0177	0.0384	-0.0208	-0.0137	0.0134	-0.0265	0.0192	-0.0212	0.335	-0.0606	0.0234	0.1026	0.0947	0.1832	-2.062	34.1274	-44.0484
7	0.5614	-0.2277	-0.192	0.1847	0.0073	0.1314	-0.0033	-0.1002	0.2345	-0.2073	0.1168	-0.1718	0.0099	0.053	0.109	0.1926	-0.0585	0.0358	0.0736	0.0529	0.0739	0.8882	23.4706	-37.9462
8	0.0005	-0.0014	0.0014	0.0029	-0.0023	0.0015	-0.0485	-0.0312	-0.063	0.0378	-0.0174	0.0244	0.0034	-0.0096	0	0.1001	-0.0049	0.0323	0.136	-0.002	0.1847	-19.2438	-14.9161	-45.1122
9	0.0435	0.0034	0.0122	0.0529	0.0007	0.0564	-0.0186	0.0134	-0.0543	-0.0213	-0.0253	0.0204	-0.0866	-0.0019	-0.0245	0.0745	0.0024	0.0087	0.0914	-0.0025	0.1105	-12.7354	-0.9808	-43.3336
10	0.0089	-0.0009	0.007	0.0102	-0.0079	0.0075	-0.0224	0.0649	-0.164	-0.0252	0.0809	-0.1402	0.0392	0.1134	-0.001	0.0969	0.0017	0.019	0.1459	-0.0349	0.1883	0.2964	-15.5878	-48.0859
11	0.0022	-0.0034	-0.0005	0.0015	0.004	0.0057	0.0108	0.0839	-0.087	-0.0646	-0.0423	-0.0884	0.0647	-0.0101	-0.0029	0.1254	0.0094	0.0338	0.1508	-0.0425	0.2021	-5.7638	-19.6915	-58.817
12	0.0035	0.0033	0.0042	0.0024	0.0014	0.0023	0.0453	0.023	-0.0012	-0.0319	-0.0095	-0.0323	-0.048	-0.022	0	0.1387	-0.0079	0.0305	0.1251	-0.0197	0.157	-8.9582	-9.4531	-59.3278
13	0.0755	0.0733	-0.0386	0.0927	-0.0422	0.0291	-0.078	0.095	-0.0654	-0.1003	-0.1009	0.0363	-0.0409	0.0011	-0.0547	0.1284	0.0156	-0.0145	0.1184	-0.0468	0.1255	-14.4502	-11.2877	-64.0564
14	0.0046	0.0055	0.0045	0.0106	0.002	0.0041	-0.0237	0.0342	0.0028	-0.0286	-0.024	0.0041	-0.0833	0.0298	-0.0442	0.4977	-0.0054	-0.1657	0.1729	0.0423	0.0901	-15.3523	11.8949	-63.9818
15	0.003	0.0083	-0.0048	0.0237	-0.018	0.0125	-0.0547	0.0606	0.0022	-0.0545	-0.0716	0.0467	-0.0333	-0.0204	-0.0143	0.1352	-0.0015	-0.039	0.1177	-0.0249	0.1432	-19.5474	-7.1456	-60.3696
16	0.3379	-0.1683	-0.1532	0.0986	0.0724	0.0974	-0.0457	0.0957	-0.0477	-0.0765	-0.1082	0.1031	-0.2281	-0.0862	-0.1572	0.2231	0.006	-0.0726	0.0941	0.0408	0.0958	-17.8657	12.0739	-50.1492

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 307 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 15 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 86 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 87 through 127 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 128 through 167 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 168 through 184 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 185 through 216 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 217 through 237 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 238 through 255 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 256 through 307 )

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