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

ID or keywords:

Entry

Database: PDB / ID: 5ucz

Title

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

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: 1.78 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ucz.cif.gz	342.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ucz.ent.gz	283.6 KB	Display	PDB format
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Validation report

Summary document	5ucz_validation.pdf.gz	451.8 KB	Display	wwPDB validaton report
Full document	5ucz_full_validation.pdf.gz	457.4 KB	Display
Data in XML	5ucz_validation.xml.gz	25 KB	Display
Data in CIF	5ucz_validation.cif.gz	35.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uc/5ucz ftp://data.pdbj.org/pub/pdb/validation_reports/uc/5ucz	HTTPS FTP

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Related structure data

Related structure data	5uckC 5ucnC 5ucpC 5ucsC 5ud0C 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjeC 5vjfC 3c4uS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ucn-d 5uck-d 3n9r-4 5ud4-d 5ud2-d 5ucp-d 1x7d-d 1wgj-d 5ud1-d 5x9i-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 (6)

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)	39.474, 86.133, 91.196
Angle α, β, γ (deg.)	90.00, 100.28, 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.26 Å³/Da / Density % sol: 45.59 %
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: Jun 17, 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: 1.78→29.911 Å / Num. obs: 54638 / % possible obs: 87.33 % / Redundancy: 3.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.08477 / Net I/σ(I): 10.86

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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: 1.78→29.911 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.9

	R_factor	Num. reflection	% reflection
R_free	0.2274	2301	4.58 %
R_work	0.1844	-	-
obs	0.1864	50202	87.35 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.78→29.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4490	0	26	320	4836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4630
X-RAY DIFFRACTION	f_angle_d	0.618	6228
X-RAY DIFFRACTION	f_dihedral_angle_d	14.52	2801
X-RAY DIFFRACTION	f_chiral_restr	0.041	686
X-RAY DIFFRACTION	f_plane_restr	0.003	806

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 (%)
1.7805-1.8192	0.4099	92	0.3445	1785	X-RAY DIFFRACTION	52
1.8192-1.8615	0.3984	103	0.3204	2044	X-RAY DIFFRACTION	60
1.8615-1.9081	0.3092	109	0.2972	2345	X-RAY DIFFRACTION	69
1.9081-1.9596	0.3225	128	0.273	2621	X-RAY DIFFRACTION	77
1.9596-2.0173	0.2995	137	0.2687	2847	X-RAY DIFFRACTION	84
2.0173-2.0824	0.3284	141	0.2568	3031	X-RAY DIFFRACTION	88
2.0824-2.1568	0.2694	146	0.2376	3079	X-RAY DIFFRACTION	90
2.1568-2.2431	0.295	158	0.2079	3147	X-RAY DIFFRACTION	93
2.2431-2.3452	0.2684	152	0.1968	3246	X-RAY DIFFRACTION	95
2.3452-2.4688	0.2338	164	0.1839	3298	X-RAY DIFFRACTION	96
2.4688-2.6234	0.2361	159	0.1802	3350	X-RAY DIFFRACTION	98
2.6234-2.8258	0.2212	161	0.1863	3352	X-RAY DIFFRACTION	98
2.8258-3.1099	0.2327	157	0.1909	3405	X-RAY DIFFRACTION	99
3.1099-3.5592	0.2325	167	0.1698	3431	X-RAY DIFFRACTION	100
3.5592-4.4818	0.1605	158	0.1385	3443	X-RAY DIFFRACTION	100
4.4818-29.9154	0.1686	169	0.1445	3477	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	0.0535	-0.1405	0.0895	0.5236	-0.2564	0.1729	-0.1216	0.48	-0.1209	0.1335	0.0464	0.0183	-0.0656	0.0147	-0.101	0.0959	-0.0334	0.0323	0.3527	-0.1415	0.175	-5.3484	-11.7801	-40.7416
2	0.0503	-0.0575	-0.0804	0.0462	0.0723	0.0968	0.0493	0.1575	0.0156	-0.0724	0.0627	-0.0888	-0.013	0.0386	0.1051	0.1295	-0.0341	0.1533	0.8317	-0.3427	0.1541	2.6412	-14.3435	-58.9638
3	0.0132	-0.024	0.034	0.019	-0.0399	0.1567	-0.0692	0.1666	-0.0485	-0.0766	-0.0239	-0.0607	-0.0507	0.0122	-0.0738	0.1994	-0.0829	0.021	0.8175	-0.0963	0.1203	-7.0914	-1.4909	-57.1575
4	0.5104	0.0465	-0.1832	0.0434	-0.0315	0.0801	-0.102	0.5251	0.064	0.1559	0.0658	0.0659	-0.3119	-0.1628	-0.0863	0.2943	0.0301	-0.0619	0.249	0.0532	0.126	-11.861	5.0941	-37.683
5	0.0046	0.0006	0.0026	0.0002	-0.0039	0.0039	-0.0322	-0.0423	-0.0509	0.0455	-0.0589	-0.0065	0.0115	0.0384	-0.0155	0.156	0.0237	-0.0115	0.252	0.1097	0.2836	7.437	-18.9272	-4.2936
6	0.0754	0.0162	0.096	0.1401	0.0555	0.1255	-0.0574	-0.1061	-0.1656	-0.0867	0.0309	0.0241	-0.0911	-0.0005	0.0064	0.1375	0.0157	0.03	0.0973	0.0284	0.2029	-1.8302	-11.6601	-13.468
7	0.004	0.0034	0.0012	0.003	0.0054	0.0125	0.0436	-0.1082	-0.0593	0.0563	0.039	0.0223	-0.0257	-0.05	0.0412	0.106	0.0325	0.0934	0.3101	0.165	0.3006	-12.5342	-19.389	2.776
8	0.0469	0.032	-0.0358	0.0509	-0.0214	0.0523	0.0581	-0.1295	-0.0712	0.0833	0.0204	0.0309	-0.0383	-0.0362	0.0624	0.1383	0.0597	0.0914	0.2989	0.1952	0.1934	-5.686	-13.0605	8.5319
9	0.0228	0.0175	-0.0096	0.0128	0.0084	0.0162	-0.0436	-0.1985	0.0364	0.009	0.0283	0.1031	-0.1783	0.0022	-0.0134	0.2152	0.0196	-0.0125	0.273	0.0963	0.195	1.2718	-3.0626	4.9802
10	0.2879	0.0467	-0.1627	0.0081	-0.0212	0.0942	-0.0654	-0.2422	0.0333	-0.038	-0.0489	-0.0146	-0.1749	0.0892	-0.0327	0.2521	-0.0352	-0.0529	0.0987	0.002	0.1441	5.8737	5.7747	-5.394
11	0.0571	0.0416	-0.0171	0.0472	0.0315	0.062	-0.0652	0.0068	0.0004	-0.1897	0.0537	-0.0635	-0.0853	0.1517	-0.0052	0.2346	-0.0705	-0.0202	-0.0004	0.0634	0.1421	6.29	3.3835	-20.4264

Refinement TLS group

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

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