PDB-4gui: 1.78 Angstrom Crystal Structure of the Salmonella enterica 3-Dehy...

ID or keywords:

Entry

Database: PDB / ID: 4gui

Title

1.78 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Quinate

Components

3-dehydroquinate dehydratase

Keywords

LYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel

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 Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Light, S.H. / Minasov, G. / Duban, M.-E. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Biochemistry / Year: 2014
Title: Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of schiff base formation.
Authors: Light, S.H. / Antanasijevic, A. / Krishna, S.N. / Caffrey, M. / Anderson, W.F. / Lavie, A.

History

Deposition	Aug 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 13, 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 / struct_ref_seq_dif / struct_site 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gui.cif.gz	209.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4gui.ent.gz	169.3 KB	Display	PDB format
PDBx/mmJSON format	4gui.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gui_validation.pdf.gz	455.3 KB	Display	wwPDB validaton report
Full document	4gui_full_validation.pdf.gz	458.6 KB	Display
Data in XML	4gui_validation.xml.gz	21.9 KB	Display
Data in CIF	4gui_validation.cif.gz	31.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/4gui ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4gui	HTTPS FTP

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Related structure data

Related structure data	4gujC 4iuoC 3l2iS 4guf 4gug 4guh C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4cno-2 4cnn-d 4cno-3 1l9w-1 4guj-d 3m7w-1 6h5c-d 4cno-4 4gug-d 3m7w-2 4cnp-d 3oex-1 6sfe-d 4clm-d 4cno-1 1l9w-2 1gqn-1 4gfs-d 3o1n-d 6h5g-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
Other databases	TargetTrack: CSGID-IDP90922

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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

A: 3-dehydroquinate dehydratase

B: 3-dehydroquinate dehydratase

hetero molecules

56 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)	48.669, 74.427, 63.135
Angle α, β, γ (deg.)	90.00, 100.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase Mass: 27629.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical	ChemComp-QIC / (1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid / Quinic acid Mass: 192.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₂O₆
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.03 Å³/Da / Density % sol: 39.53 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal ...Details: protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal incubated in and frozen from 5 M sodium quinate, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal

Density Matthews: 2.03 Å³/Da / Density % sol: 39.53 %

Crystal grow

Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2012 / Details: Beryllium lens
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 1.78→30 Å / Num. all: 41378 / Num. obs: 41378 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / R_merge(I) obs: 0.056 / Net I/σ(I): 17.5
Reflection shell	Resolution: 1.78→1.81 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.314 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2109 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L2I

3l2i

Resolution: 1.78→28.66 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / SU B: 5.325 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18801	2100	5.1 %	RANDOM
R_work	0.15927	-	-	-
all	0.16079	39202	-	-
obs	0.16079	39202	97.22 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.08 Å²	0 Å²	3.42 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	-0.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→28.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3818	0	32	239	4089

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	3943
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3903
X-RAY DIFFRACTION	r_angle_refined_deg	1.351	1.973	5363
X-RAY DIFFRACTION	r_angle_other_deg	0.727	3	8980
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.128	5	514
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.743	24.522	157
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.917	15	698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.821	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	660
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4422
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	818
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.78→1.826 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	154	-
R_work	0.244	2917	-
obs	-	-	99.29 %

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	13.5771	8.0367	3.4177	16.6756	3.8753	7.4122	0.1385	-0.3083	-0.1154	0.9764	0.0617	-0.3306	0.1382	0.6081	-0.2003	0.17	0.0319	-0.1086	0.173	-0.0012	0.0988	-7.1936	-6.1035	32.8283
2	3.2585	0.5534	-0.6835	2.4791	0.1816	1.069	-0.0564	0.0009	-0.2457	-0.0191	-0.0523	0.1455	0.108	-0.1594	0.1087	0.122	-0.0304	-0.084	0.1399	-0.0214	0.1147	-21.833	-10.3745	21.2656
3	13.3842	-9.371	-2.1351	11.3383	2.5641	4.1564	-0.1646	-0.5663	-0.1228	0.4198	0.1416	0.3553	0.2619	-0.2787	0.023	0.0649	-0.0413	-0.0119	0.0733	0.0095	0.0392	-27.9768	-13.7879	29.0032
4	3.4385	-0.3771	-0.2484	2.1162	-0.8806	1.3887	-0.1087	-0.0319	0.0721	0.0637	0.0657	0.2252	0.0253	-0.1078	0.043	0.1217	-0.0028	-0.088	0.1932	-0.0451	0.1421	-25.7759	0.2067	24.835
5	2.1201	-0.5338	-1.2244	1.6334	0.2911	2.9256	0.0426	-0.258	0.1603	0.3517	-0.0587	0.1305	-0.0912	-0.1516	0.016	0.1869	-0.0067	-0.0607	0.2654	-0.0527	0.1461	-23.9013	2.5529	34.5486
6	1.0896	0.8588	-1.0946	1.5396	-0.984	2.3348	0.1216	-0.1794	0.2501	0.2248	0.0012	0.1053	-0.1544	-0.0127	-0.1228	0.1274	0.0043	-0.0692	0.1628	-0.0534	0.1524	-15.2452	9.4362	25.5641
7	1.5772	0.2769	-0.7036	0.9664	-0.388	2.5968	0.0562	-0.1277	0.23	0.1227	0.023	-0.0441	-0.2087	-0.0271	-0.0792	0.1022	-0.003	-0.0865	0.1344	-0.0407	0.1414	-9.4001	10.4591	21.5647
8	4.0937	1.2665	3.2846	1.7045	0.9935	12.3345	-0.1019	-0.2804	0.2554	0.1935	-0.1267	-0.0722	-0.4189	0.6326	0.2286	0.0965	-0.0068	-0.0828	0.1203	-0.0405	0.091	-5.4046	7.8463	27.463
9	1.8509	0.9146	-0.7223	3.4722	-0.0676	1.0417	-0.0585	0.0494	-0.0521	-0.3863	0.067	-0.1023	0.0345	-0.025	-0.0085	0.1247	-0.0208	-0.0676	0.1037	-0.0129	0.0862	-10.549	-1.3091	13.9241
10	7.0872	-0.6866	0.9219	2.8634	-3.3601	4.0158	-0.2755	-0.049	-0.161	-0.1012	0.0716	-0.2409	0.1669	-0.0079	0.2039	0.1203	0.0026	-0.0464	0.1155	-0.0646	0.1585	-1.5582	-8.7752	15.154
11	3.7347	-1.1499	0.2537	3.2132	-2.3032	2.2638	-0.0804	0.3337	-0.1456	-0.2879	0.048	0.2089	0.1704	-0.3057	0.0324	0.1536	-0.029	-0.112	0.1494	-0.0517	0.1224	6.6772	-0.4919	-7.6971
12	3.9076	1.0075	1.7084	7.6301	1.428	1.7137	-0.0446	0.2166	-0.2748	0.3738	-0.004	0.0961	0.2277	0.0124	0.0485	0.1763	-0.0099	-0.0708	0.0849	-0.0117	0.189	25.6786	-12.3148	-1.9385
13	10.3824	2.1099	0.4362	2.5851	1.5188	0.9821	-0.0307	0.081	-0.4538	0.3209	0.0029	-0.0671	0.1787	-0.0091	0.0278	0.1434	-0.0042	-0.0731	0.0281	0.006	0.088	20.3653	-5.3358	-2.1035
14	14.2715	5.5011	3.0467	6.8274	2.3261	3.8727	-0.0974	0.3338	0.429	-0.2016	0.0156	0.0591	0.1704	0.1898	0.0819	0.0883	0.0393	-0.0585	0.0386	-0.0103	0.0729	28.2	-6.5947	-9.6517
15	1.6263	0.51	0.3656	3.0567	1.0331	2.2241	-0.0046	0.0176	0.0296	0.0838	-0.0181	-0.1319	0.1001	0.0595	0.0227	0.0981	0.0121	-0.0905	0.0497	0.0018	0.0957	25.1528	3.9857	-6.3152
16	1.4329	-0.1631	-0.9624	0.5347	-0.1815	1.4052	0.1232	-0.0301	0.1605	-0.0358	-0.0489	-0.0348	-0.1453	-0.0596	-0.0743	0.1139	-0.0027	-0.0853	0.0683	0.0019	0.1221	14.3638	13.024	0.4923
17	10.0209	-3.0723	-6.2692	20.6224	-15.8827	20.0471	0.0168	0.4449	0.3525	0.1672	0.2635	-0.0349	-0.156	-0.6954	-0.2803	0.108	-0.0199	-0.1098	0.2108	-0.0127	0.1455	1.129	17.5461	0.1453
18	5.3712	-2.3601	1.2896	3.2092	-2.842	11.6975	-0.0441	0.2723	0.3254	-0.198	-0.1728	-0.1263	0.2605	-0.5111	0.2169	0.0823	-0.0006	-0.0775	0.0713	0.0026	0.1145	7.2817	9.804	-2.7519
19	1.5902	-0.1373	-0.243	2.6321	-0.8613	2.3306	0.0552	-0.0838	-0.0445	0.0878	-0.071	0.0387	0.0734	0.0243	0.0158	0.0816	-0.0203	-0.0813	0.0922	-0.0092	0.1068	6.6271	1.309	7.6762
20	6.319	-1.5101	2.6576	5.8549	-1.065	4.9808	-0.1954	0.0716	-0.1474	0.1489	-0.0544	-0.3258	0.179	0.3382	0.2498	0.11	-0.0115	-0.0568	0.119	0.0071	0.1375	5.7463	-7.7174	6.3195

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 12
2	X-RAY DIFFRACTION	2	A	13 - 56
3	X-RAY DIFFRACTION	3	A	57 - 73
4	X-RAY DIFFRACTION	4	A	74 - 96
5	X-RAY DIFFRACTION	5	A	97 - 132
6	X-RAY DIFFRACTION	6	A	133 - 158
7	X-RAY DIFFRACTION	7	A	159 - 191
8	X-RAY DIFFRACTION	8	A	192 - 204
9	X-RAY DIFFRACTION	9	A	205 - 238
10	X-RAY DIFFRACTION	10	A	239 - 252
11	X-RAY DIFFRACTION	11	B	2 - 21
12	X-RAY DIFFRACTION	12	B	22 - 38
13	X-RAY DIFFRACTION	13	B	39 - 53
14	X-RAY DIFFRACTION	14	B	54 - 73
15	X-RAY DIFFRACTION	15	B	74 - 114
16	X-RAY DIFFRACTION	16	B	115 - 189
17	X-RAY DIFFRACTION	17	B	190 - 195
18	X-RAY DIFFRACTION	18	B	196 - 203
19	X-RAY DIFFRACTION	19	B	204 - 228
20	X-RAY DIFFRACTION	20	B	229 - 252

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