PDB-4gfs: 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratas...

ID or keywords:

Entry

Database: PDB / ID: 4gfs

Title

1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at Active Site

Components

3-dehydroquinate dehydratase

Keywords

LYASE /

Structural Genomics / 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: 1.8 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at Active Site
Authors: Light, S.H. / Minasov, G. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F.

History

Deposition	Aug 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gf/4gfs ftp://data.pdbj.org/pub/pdb/validation_reports/gf/4gfs	HTTPS FTP

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Related structure data

Related structure data	3l2iS 3lb0 3m7w 3o1n 3oex 3s42 S: Starting model for refinement
Similar structure data	4cnp-d 1l9w-2 3m7w-1 3l2i-d 4cno-3 3m7w-2 4guj-d 4cno-2 1gqn-1 1l9w-1 4gui-d 6h5j-1 4cno-4 3m7w-3 3js3-1 1qfe-d 6sfe-d 6h5c-d 4cnn-d 3oex-2 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: 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

55.7 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)	48.679, 74.468, 63.566
Angle α, β, γ (deg.)	90.00, 100.17, 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 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.05 Å³/Da / Density % sol: 40.06 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution: 7.5 mg/m, 0.50 sodium phthalate, 0.01 M Tris-HCl (pH 8.3) Screen solution: PEGs II B8 (Qiagen), 0.1 Nickel chloride, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME , VAPOR ...Details: Protein solution: 7.5 mg/m, 0.50 sodium phthalate, 0.01 M Tris-HCl (pH 8.3) Screen solution: PEGs II B8 (Qiagen), 0.1 Nickel chloride, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal

Density Matthews: 2.05 Å³/Da / Density % sol: 40.06 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 7.5 mg/m, 0.50 sodium phthalate, 0.01 M Tris-HCl (pH 8.3) Screen solution: PEGs II B8 (Qiagen), 0.1 Nickel chloride, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME , VAPOR ...

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Data collection

Diffraction	Mean temperature: 295 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2012 / Details: Beryllium lens
Radiation	Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 40064 / Num. obs: 40064 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_merge(I) obs: 0.078 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.567 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1735 / % possible all: 86.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L2I

3l2i

Resolution: 1.8→29.4 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / SU B: 9.311 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24925	2027	5.1 %	RANDOM
R_work	0.19878	-	-	-
all	0.20136	38018	-	-
obs	0.20136	38018	96.79 %	-

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: 39.789 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.16 Å²	-0 Å²	3.37 Å²
2-	-	-1.57 Å²	-0 Å²
3-	-	-	4.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3806	0	14	193	4013

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	3946
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3893
X-RAY DIFFRACTION	r_angle_refined_deg	1.763	1.964	5362
X-RAY DIFFRACTION	r_angle_other_deg	0.845	3	8955
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.548	5	516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.231	24.568	162
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.846	15	702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.992	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	650
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4465
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	833
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: 1.801→1.848 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	124	-
R_work	0.346	2450	-
obs	-	-	85.4 %

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	2.7044	-6.4617	0.649	16.4325	-1.1025	0.3777	-0.5332	-0.3292	0.0467	0.5267	0.6812	-0.3748	-0.4357	-0.0129	-0.148	0.6881	0.0309	0.0432	0.535	-0.0167	0.1974	-6.7846	-3.4058	35.636
2	3.4524	-0.697	-1.7359	1.5476	1.5505	1.9438	-0.112	-0.1407	-0.1954	0.3356	0.0398	-0.0215	0.2442	0.1594	0.0723	0.2926	-0.0278	-0.1066	0.2439	-0.0107	0.0637	-10.3287	-8.5384	26.0078
3	14.5696	-3.1474	-0.0491	1.127	0.8919	1.9074	-0.0675	0.0025	-0.8555	-0.1093	-0.1784	0.3461	-0.0698	-0.3496	0.2459	0.2316	-0.0317	-0.0947	0.3171	-0.1229	0.154	-28.9773	-15.8066	19.6753
4	5.6779	-0.8022	-0.3983	3.3185	0.7782	0.3314	-0.0305	-0.1406	-0.4267	0.0844	-0.1842	0.4728	0.0599	-0.1665	0.2148	0.2698	-0.0648	-0.0372	0.319	-0.1063	0.1637	-24.2877	-9.8603	23.5371
5	1.5861	-0.4579	-0.4763	2.3223	0.273	1.2012	0.0721	-0.0661	0.0191	0.172	-0.1595	0.237	0.0775	-0.1051	0.0874	0.1915	-0.0356	-0.0302	0.2592	-0.1027	0.0793	-24.339	-2.2205	31.5343
6	1.4347	0.6499	-1.1145	1.6192	-0.4291	1.5269	0.0722	-0.1529	0.1971	0.1468	-0.0743	0.0987	-0.1479	-0.1445	0.0021	0.1821	0.0068	-0.0726	0.2342	-0.081	0.0872	-10.5519	10.9905	22.189
7	0.7844	0.1458	0.4447	2.1692	0.4467	1.5561	0.0077	-0.2117	0.1287	0.0443	-0.117	0.043	0.0618	-0.2058	0.1093	0.2532	-0.0286	-0.0718	0.2964	-0.0363	0.0445	-8.9955	1.1934	18.7697
8	3.1988	-1.7769	-1.5917	3.3638	-1.4181	3.0339	-0.171	0.0504	-0.0877	0.0513	-0.024	-0.123	0.082	-0.0624	0.195	0.2373	-0.0178	-0.0446	0.2585	-0.0402	0.0905	-3.2635	-8.6971	15.1232
9	3.1132	-0.0541	0.6213	2.0071	-0.3359	0.3035	0.0279	0.2116	0.034	-0.2935	-0.0233	0.1606	0.1241	-0.0953	-0.0046	0.327	-0.0056	-0.1155	0.3003	-0.0156	0.0622	8.0094	-0.837	-6.7648
10	6.2608	-1.9775	-0.0972	2.5578	0.3424	1.1526	-0.0777	0.1395	-0.6957	0.0609	-0.0267	0.067	-0.0195	-0.0271	0.1043	0.1953	-0.0171	-0.0593	0.1427	-0.0083	0.1223	21.576	-11.396	-2.6183
11	9.1156	0.4464	-4.3272	3.0569	0.7525	3.7184	0.0092	-0.1269	0.277	0.3176	0.1062	-0.3386	0.2433	0.1856	-0.1155	0.244	0.0293	-0.1147	0.2223	0.0083	0.1064	31.7388	-1.9053	-3.7392
12	3.0496	1.5468	3.6153	4.4038	2.3663	5.3509	0.0723	0.2366	-0.2285	-0.2048	-0.0157	0.0498	0.1242	-0.0882	-0.0566	0.2956	-0.001	-0.1332	0.2569	-0.0628	0.1343	23.6793	-9.9002	-10.6017
13	1.5219	0.1968	-0.4621	2.0389	0.3359	1.1807	0.0592	0.0115	0.0703	-0.0613	-0.0381	-0.12	0.001	-0.0121	-0.0211	0.2194	0.0073	-0.0851	0.1983	0.0057	0.0529	22.8954	7.0017	-7.0113
14	1.55	-0.1331	-0.8835	1.4425	-0.266	0.7811	0.1438	-0.1427	0.2362	0.0558	-0.0171	-0.0186	-0.0669	0.0327	-0.1267	0.2001	-0.0287	-0.0697	0.192	-0.0416	0.087	8.7919	11.9438	5.4161
15	3.301	-1.6223	-1.3299	6.2595	-1.4793	1.5208	-0.006	-0.0119	0.0594	0.1637	0.009	-0.0361	-0.0489	0.1467	-0.003	0.2497	-0.015	-0.0954	0.2448	-0.0068	0.0489	6.7662	-1.1715	5.6148
16	5.7626	-1.1747	2.1094	3.3761	-2.0378	3.0913	-0.2697	-0.1053	-0.2028	0.1502	0.0332	0.3466	0.0262	0.2133	0.2365	0.3055	0.0023	-0.0589	0.3334	0.0347	0.2599	1.9566	-7.1269	5.3735

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 6
2	X-RAY DIFFRACTION	2	A	7 - 23
3	X-RAY DIFFRACTION	3	A	24 - 36
4	X-RAY DIFFRACTION	4	A	37 - 59
5	X-RAY DIFFRACTION	5	A	60 - 139
6	X-RAY DIFFRACTION	6	A	140 - 193
7	X-RAY DIFFRACTION	7	A	194 - 235
8	X-RAY DIFFRACTION	8	A	236 - 252
9	X-RAY DIFFRACTION	9	B	1 - 23
10	X-RAY DIFFRACTION	10	B	24 - 47
11	X-RAY DIFFRACTION	11	B	48 - 60
12	X-RAY DIFFRACTION	12	B	61 - 74
13	X-RAY DIFFRACTION	13	B	75 - 145
14	X-RAY DIFFRACTION	14	B	146 - 213
15	X-RAY DIFFRACTION	15	B	214 - 234
16	X-RAY DIFFRACTION	16	B	235 - 252

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