PDB-8b2c: Crystal structure of type I dehydroquinase from Salmonella typhi ...

ID or keywords:

Entry

Database: PDB / ID: 8b2c

Title

Crystal structure of type I dehydroquinase from Salmonella typhi inhibited by an epoxide derivative

Components

3-dehydroquinate dehydratase

Keywords

LYASE / CHORISMATE BIOSYNTHETIC PROCESS / 3-DEHYDROQUINASE

Function / homology

Function and homology information

3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Otero, J.M. / Rodriguez, A. / Maneiro, M. / Lence, E. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.

Funding support

Spain, 2items

Citation

Journal: Front Mol Biosci / Year: 2023
Title: Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight.
Authors: Rodriguez, A. / Maneiro, M. / Lence, E. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.

History

Deposition	Sep 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8b2c.cif.gz	69.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8b2c.ent.gz		Display	PDB format
PDBx/mmJSON format	8b2c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/8b2c ftp://data.pdbj.org/pub/pdb/validation_reports/b2/8b2c	HTTPS FTP

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Related structure data

Related structure data	8b2aC 8b2bC 4cnnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

AAA: 3-dehydroquinate dehydratase

hetero molecules

28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	42.713, 47.080, 105.200
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase / Type I dehydroquinase / DHQ1 Mass: 27680.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase
#2: Chemical	ChemComp-OVU / (1~{S},2~{R},4~{R},5~{S},6~{S})-2,4,5-trihydroxy-7-oxabicyclo[4.1.0]heptane-2-carboxylic acid Mass: 190.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₀O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 26 % (w/v) PEG 2000 MME, 0.1 M HEPES-NaOH

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00556 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00556 Å / Relative weight: 1
Reflection	Resolution: 1.55→105.2 Å / Num. obs: 28123 / % possible obs: 89.4 % / Redundancy: 4.1 % / B_iso Wilson estimate: 13.361 Å² / CC_1/2: 1 / R_merge(I) obs: 0.036 / R_pim(I) all: 0.019 / R_rim(I) all: 0.041 / Net I/σ(I): 22.6
Reflection shell	Resolution: 1.55→1.63 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3317 / CC_1/2: 0.903 / R_pim(I) all: 0.209 / R_rim(I) all: 0.452 / % possible all: 73.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	November 3, 2014	data reduction
SCALA	3.3.22	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4CNN

4cnn

Resolution: 1.55→52.6 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / SU B: 1.666 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1997	1366	4.879 %
R_work	0.1668	26630	-
all	0.168	-	-
obs	-	27996	88.595 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 16.196 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.236 Å²	-0 Å²	-0 Å²
2-	-	-0.358 Å²	0 Å²
3-	-	-	0.594 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→52.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1936	0	38	128	2102

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2032
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1975
X-RAY DIFFRACTION	r_angle_refined_deg	1.758	1.646	2764
X-RAY DIFFRACTION	r_angle_other_deg	1.52	1.581	4546
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.647	5	259
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.77	22.268	97
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.299	15	358
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.107	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	284
X-RAY DIFFRACTION	r_chiral_restr_other	0.024	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2258
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	432
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	386
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	1903
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	981
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1041
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.001	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	92
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	22
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.094	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.426	1.517	1015
X-RAY DIFFRACTION	r_mcbond_other	1.358	1.512	1014
X-RAY DIFFRACTION	r_mcangle_it	2.119	2.272	1269
X-RAY DIFFRACTION	r_mcangle_other	2.13	2.276	1270
X-RAY DIFFRACTION	r_scbond_it	2.421	1.82	1017
X-RAY DIFFRACTION	r_scbond_other	2.338	1.804	1007
X-RAY DIFFRACTION	r_scangle_it	3.604	2.624	1487
X-RAY DIFFRACTION	r_scangle_other	3.554	2.603	1476
X-RAY DIFFRACTION	r_lrange_it	4.484	18.907	2174
X-RAY DIFFRACTION	r_lrange_other	4.455	18.803	2159

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.55-1.59	0.244	91	0.222	1541	0.224	2300	0.891	0.886	70.9565	0.196
1.59-1.634	0.249	88	0.205	1588	0.207	2234	0.906	0.92	75.0224	0.173
1.634-1.681	0.249	66	0.196	1620	0.199	2173	0.914	0.925	77.5886	0.163
1.681-1.733	0.225	94	0.189	1626	0.191	2115	0.918	0.935	81.3239	0.156
1.733-1.79	0.25	74	0.194	1651	0.196	2048	0.906	0.928	84.2285	0.159
1.79-1.852	0.221	92	0.18	1663	0.182	1996	0.937	0.944	87.9258	0.148
1.852-1.922	0.253	88	0.175	1669	0.179	1936	0.933	0.951	90.7541	0.144
1.922-2	0.215	82	0.175	1620	0.177	1837	0.936	0.949	92.6511	0.143
2-2.089	0.222	67	0.168	1587	0.17	1784	0.943	0.955	92.713	0.142
2.089-2.191	0.191	74	0.168	1536	0.169	1720	0.951	0.958	93.6047	0.143
2.191-2.309	0.226	86	0.175	1476	0.178	1623	0.931	0.95	96.2415	0.152
2.309-2.449	0.209	77	0.161	1418	0.164	1556	0.946	0.958	96.0797	0.143
2.449-2.618	0.219	78	0.165	1328	0.168	1464	0.951	0.955	96.0383	0.15
2.618-2.827	0.182	58	0.166	1243	0.167	1353	0.949	0.961	96.1567	0.154
2.827-3.096	0.189	48	0.166	1187	0.167	1262	0.949	0.962	97.8605	0.161
3.096-3.46	0.164	54	0.159	1063	0.16	1149	0.968	0.97	97.215	0.159
3.46-3.992	0.182	51	0.146	956	0.148	1039	0.962	0.972	96.9201	0.153
3.992-4.882	0.156	40	0.135	819	0.136	880	0.981	0.98	97.6136	0.145
4.882-6.875	0.188	32	0.179	660	0.179	702	0.968	0.972	98.5755	0.191
6.875-52.6	0.171	26	0.164	379	0.164	429	0.976	0.975	94.4056	0.183

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