PDB-4guj: 1.50 Angstrom Crystal Structure of the Salmonella enterica 3-Dehy...

ID or keywords:

Entry

Database: PDB / ID: 4guj

Title

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

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: 1.5 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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PDBx/mmCIF format	4guj.cif.gz	215.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4guj.ent.gz	173.9 KB	Display	PDB format
PDBx/mmJSON format	4guj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4guj_validation.pdf.gz	450.9 KB	Display	wwPDB validaton report
Full document	4guj_full_validation.pdf.gz	453.9 KB	Display
Data in XML	4guj_validation.xml.gz	24.5 KB	Display
Data in CIF	4guj_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/4guj ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4guj	HTTPS FTP

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Related structure data

Related structure data	4guiC 4iuoC 3l2iS 4guf 4gug 4guh C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6h5c-d 4cnn-d 3oex-1 4cnp-d 1l9w-1 4gui-d 4cno-2 4gug-d 6sfe-d 3o1n-d 1gqn-1 1qfe-d 4cno-3 4gfs-d 3l2i-d 4clm-d 6h5g-1 3m7w-2 3m7w-1 4cno-4 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

55.8 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)	48.620, 74.966, 63.042
Angle α, β, γ (deg.)	90.00, 100.49, 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-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₀O₅
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.04 Å³/Da / Density % sol: 39.83 %
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 2 M sodium shikimate, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.83 %

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-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2012 / Details: Beryllium lens
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.5→30 Å / Num. all: 69175 / Num. obs: 69175 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / R_merge(I) obs: 0.045 / Net I/σ(I): 25.5
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.367 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3375 / % possible all: 94.5

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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: 1.5→28.66 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.964 / SU B: 2.596 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / 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	0.18237	3483	5.1 %	RANDOM
R_work	0.15534	-	-	-
all	0.15674	65443	-	-
obs	0.15674	65443	96.85 %	-

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: 20.966 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.96 Å²	0 Å²	1.7 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	1.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→28.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3818	0	27	420	4265

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	4014
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3991
X-RAY DIFFRACTION	r_angle_refined_deg	1.421	1.973	5472
X-RAY DIFFRACTION	r_angle_other_deg	0.737	3	9192
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.547	5	536
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.58	24.465	159
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.8	15	718
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.25	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	675
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4536
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	839
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: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.223	223	-
R_work	0.215	4760	-
obs	-	-	94.99 %

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	12.2396	2.0989	0.6457	4.3094	1.3191	1.658	-0.0424	-0.4008	-0.5137	0.6648	0.1252	-0.3941	0.2665	0.272	-0.0828	0.1921	0.0338	-0.0907	0.1866	-0.0041	0.0739	29.5862	-6.4268	94.9594
2	5.1781	1.2916	0.8031	2.365	0.4952	1.0777	-0.0745	-0.0467	-0.241	-0.0006	0.0384	0.0072	0.0576	-0.0096	0.0361	0.0995	-0.0057	-0.0121	0.0508	-0.0052	0.0244	16.6444	-11.4201	82.5687
3	6.1968	-1.0324	-0.7685	2.1571	-0.2231	0.4063	-0.1206	0.0024	-0.4606	-0.0644	0.0316	0.0649	0.0801	-0.0782	0.0889	0.1106	-0.0129	-0.0109	0.0693	-0.022	0.0483	14.5133	-9.3361	84.0848
4	10.2126	-6.6857	-0.5771	7.8247	0.0567	1.4	-0.2335	-0.3203	-0.2614	0.5295	0.1552	0.2523	0.1589	-0.1282	0.0783	0.0945	-0.0154	0.0166	0.0389	0.0044	0.0194	8.4992	-13.3476	90.9501
5	1.7902	0.0186	-0.5356	1.5016	0.0801	1.0046	-0.0466	-0.1586	0.0995	0.1198	0.0571	0.0787	0.014	-0.0383	-0.0105	0.1009	0.011	-0.0235	0.0786	-0.0224	0.022	11.8204	0.811	91.1183
6	5.0188	-2.1993	0.1042	7.1408	-0.9809	2.8978	-0.0252	-0.419	0.2214	0.4079	-0.0631	0.0087	-0.053	0.0882	0.0883	0.173	0.0141	-0.0197	0.1594	-0.0542	0.0273	15.3947	3.2271	101.7961
7	1.5625	0.4276	-0.6628	0.5512	-0.4757	1.3932	0.0608	-0.0696	0.2633	0.1168	0.0306	0.0197	-0.1276	0.0533	-0.0914	0.1033	-0.0015	-0.0296	0.0669	-0.0375	0.0702	23.1923	10.3669	86.981
8	2.4157	0.1805	-0.1447	1.1765	-0.4779	6.3147	0.0152	0.0318	0.2007	-0.005	-0.0174	-0.0684	0.0092	0.1943	0.0022	0.0349	-0.0138	-0.0151	0.0316	-0.005	0.0431	32.0764	11.6789	77.7981
9	1.7167	0.448	-0.2697	1.4964	-0.5362	1.4303	-0.0605	-0.0423	0.1039	-0.018	-0.0238	-0.1708	-0.0065	0.1202	0.0843	0.0689	-0.0141	-0.0281	0.0614	-0.011	0.0516	30.3097	5.0857	81.7822
10	2.1324	0.4211	-1.4555	1.1348	-0.2568	1.03	-0.1919	0.0995	-0.2052	-0.1324	0.0734	-0.1695	0.1078	-0.0247	0.1185	0.0995	-0.022	0.0033	0.0589	-0.0402	0.059	29.4574	-5.7255	77.1525
11	9.992	-5.197	0.128	9.8842	-0.3702	1.4474	0.1775	0.6155	-0.1072	-0.9107	-0.2174	0.0273	0.1217	-0.3809	0.04	0.216	-0.043	-0.0709	0.2169	-0.0189	0.0651	44.1748	1.5523	49.9271
12	6.914	-2.0702	-0.1195	1.8096	0.3941	0.3541	-0.0735	0.1574	-0.3994	0.1252	0.012	0.0809	0.0981	-0.0588	0.0615	0.1239	-0.0186	-0.0141	0.0664	-0.0054	0.0677	56.2121	-8.7338	59.8673
13	7.8628	0.407	-0.3784	1.5657	0.531	0.7568	-0.1161	0.1447	-0.4818	0.1695	0.0418	-0.0174	0.1026	-0.0326	0.0743	0.1279	-0.0067	-0.0185	0.0231	-0.0026	0.0458	56.8149	-5.3085	59.7065
14	8.2754	2.9411	0.3021	4.4722	2.2234	3.1785	0.0677	0.3758	0.1797	-0.1635	0.0058	0.0906	0.1009	0.2669	-0.0735	0.1177	0.0515	-0.0739	0.0811	-0.0124	0.0571	66.9226	-5.8263	52.6287
15	4.0208	1.5438	1.2755	4.3793	1.435	1.9104	0.0109	0.0793	-0.1226	0.0975	0.0015	-0.0417	0.081	-0.0213	-0.0124	0.1014	0.0027	-0.0321	0.0235	-0.0028	0.0157	57.8628	-0.7011	57.3922
16	0.9875	0.0055	-0.1755	2.4271	0.6623	1.529	0.0842	0.1006	0.1012	-0.0683	-0.016	-0.1264	-0.0179	0.0395	-0.0682	0.1007	0.0048	-0.0138	0.0356	0.0081	0.0251	61.1599	8.6739	52.8981
17	1.0755	0.0042	-0.2736	0.5895	-0.3514	1.0963	0.0605	-0.0814	0.1125	-0.0033	0.0103	-0.0024	-0.0633	-0.0597	-0.0708	0.0702	-0.0086	-0.0207	0.035	-0.0036	0.0285	48.6652	13.5857	67.9022
18	12.086	2.2075	-8.4923	15.3733	-8.3454	12.9087	0.0644	0.2667	0.3627	0.1652	0.2237	-0.1653	-0.0254	-0.6874	-0.288	0.0589	0.006	-0.0518	0.0999	0.04	0.0834	38.4215	17.8735	61.8586
19	1.5793	0.3033	-0.4509	1.1663	-0.4796	1.295	0.0222	-0.0591	-0.0785	0.0043	-0.0665	-0.0476	0.1079	0.0046	0.0443	0.0768	-0.0132	-0.0323	0.05	0.0005	0.023	45.5584	1.6146	67.9004
20	4.6749	0.5771	0.5948	3.2782	-1.2873	5.0094	-0.2979	0.2261	-0.1232	0.018	0.016	0.0989	0.2063	-0.0477	0.2819	0.0682	-0.0259	0.0039	0.0597	-0.0187	0.0605	39.1888	-6.5168	66.9216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 11
2	X-RAY DIFFRACTION	2	A	12 - 37
3	X-RAY DIFFRACTION	3	A	38 - 55
4	X-RAY DIFFRACTION	4	A	56 - 73
5	X-RAY DIFFRACTION	5	A	74 - 122
6	X-RAY DIFFRACTION	6	A	123 - 135
7	X-RAY DIFFRACTION	7	A	136 - 175
8	X-RAY DIFFRACTION	8	A	176 - 192
9	X-RAY DIFFRACTION	9	A	193 - 217
10	X-RAY DIFFRACTION	10	A	218 - 252
11	X-RAY DIFFRACTION	11	B	2 - 11
12	X-RAY DIFFRACTION	12	B	12 - 38
13	X-RAY DIFFRACTION	13	B	39 - 52
14	X-RAY DIFFRACTION	14	B	53 - 71
15	X-RAY DIFFRACTION	15	B	72 - 85
16	X-RAY DIFFRACTION	16	B	86 - 139
17	X-RAY DIFFRACTION	17	B	140 - 189
18	X-RAY DIFFRACTION	18	B	190 - 195
19	X-RAY DIFFRACTION	19	B	196 - 234
20	X-RAY DIFFRACTION	20	B	235 - 252

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