PDB-4guf: 1.5 Angstrom Crystal Structure of the Salmonella enterica 3-Dehyd...

ID or keywords:

Entry

Database: PDB / ID: 4guf

Title

1.5 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant

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: Protein Sci. / Year: 2013
Title: Reassessing the type I dehydroquinate dehydratase catalytic triad: Kinetic and structural studies of Glu86 mutants.
Authors: Light, S.H. / 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	Feb 6, 2013	Group: Database references
Revision 1.2	Apr 3, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	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 / 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 / _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	4guf.cif.gz	225.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4guf.ent.gz	180.7 KB	Display	PDB format
PDBx/mmJSON format	4guf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4guf_validation.pdf.gz	439.2 KB	Display	wwPDB validaton report
Full document	4guf_full_validation.pdf.gz	444.1 KB	Display
Data in XML	4guf_validation.xml.gz	25.9 KB	Display
Data in CIF	4guf_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/4guf ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4guf	HTTPS FTP

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Related structure data

Related structure data	4gugC 4guhC 3l2iS 4gui 4guj C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6sfe-d 3oex-1 6h5c-d 4guj-d 3o1n-d 6h5g-1 5tnd-2 4gug-d 3js3-1 3l2i-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
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

60.1 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)	36.771, 45.552, 81.059
Angle α, β, γ (deg.)	93.90, 101.41, 105.90
Int Tables number	1
Space group name H-M	P1

#1: Protein	3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase Mass: 30043.273 Da / Num. of mol.: 2 / Mutation: E86A 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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.11 Å³/Da / Density % sol: 41.77 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG E6 (0.2 M sodium chloride, 20% w/v PEG3350), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2012 / Details: Bimorph K-B pair
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.5→30 Å / Num. all: 74606 / Num. obs: 74606 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / R_merge(I) obs: 0.056 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3584 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	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: 1.5→29.43 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.636 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / 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	0.19121	3730	5 %	RANDOM
R_work	0.16659	-	-	-
all	0.16783	74606	-	-
obs	0.16783	70854	94.66 %	-

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: 21.749 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	0.79 Å²	-0.21 Å²
2-	-	1.27 Å²	-0.69 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→29.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3882	0	1	548	4431

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	4175
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4162
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.965	5707
X-RAY DIFFRACTION	r_angle_other_deg	0.739	3	9591
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.57	5	568
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.291	24.471	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.277	15	765
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.945	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	699
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4770
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	896
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	0.251	245	-
R_work	0.238	4828	-
obs	-	-	86.47 %

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	5.6462	1.4058	2.1205	4.5922	0.008	5.5502	0.0923	-0.2692	-0.108	0.1713	-0.1327	-0.162	0.2307	0.149	0.0404	0.0453	-0.0131	0.0048	0.1191	0.0438	0.0321	3.7586	-3.1374	6.3795
2	5.6223	-0.1575	-5.4099	0.4586	-0.3221	6.3388	-0.143	-0.0394	0.0538	-0.0434	0.1508	0.0509	0.3439	-0.018	-0.0078	0.1404	-0.0293	-0.0093	0.0869	0.0329	0.0437	-15.7699	-11.3327	8.0295
3	9.9156	5.3434	-5.4103	5.2222	-3.5927	4.4126	-0.3063	-0.147	-0.7187	0.0648	-0.1768	-0.1096	0.5757	0.2963	0.483	0.2834	0.0225	0.0832	0.0596	0.0415	0.1242	-10.7697	-17.0666	6.4682
4	2.3771	0.3199	-1.1113	1.4383	-0.6744	2.4747	-0.0742	-0.1029	-0.0287	0.0696	0.033	0.0618	0.0722	-0.0003	0.0412	0.0614	-0.0263	0.0046	0.0774	0.037	0.0262	-16.3126	-4.9195	13.4365
5	1.9844	-0.2215	0.2219	2.1224	0.0573	2.3354	0.0488	-0.2141	0.1882	0.1599	-0.0473	-0.0309	-0.3291	0.1495	-0.0015	0.1132	-0.0445	0.0061	0.1076	-0.0115	0.0335	-10.0214	6.481	13.9011
6	0.9747	0.1717	0.3424	0.5634	0.4088	3.2661	-0.0175	-0.0212	0.0912	-0.0216	-0.0385	0.0198	-0.2853	-0.1716	0.056	0.0652	-0.0044	-0.0023	0.0579	0.0161	0.0361	-10.7235	7.7181	-7.0201
7	4.5797	1.3575	2.6597	2.4261	1.4083	4.4859	0.1034	0.0167	0.1724	-0.0179	-0.143	0.0543	0.0822	-0.0327	0.0396	0.0544	-0.0021	0.0168	0.0611	0.0278	0.0288	-8.0099	1.5272	-7.7607
8	0.9349	1.3861	-0.1586	2.6821	1.0753	2.8643	-0.0691	0.0595	0.0114	0.0653	0.093	0.0106	0.3172	0.0352	-0.0239	0.1486	-0.0063	0.0045	0.0747	0.0376	0.0281	-6.7905	-10.8221	-8.0478
9	3.6527	-1.2202	2.3394	1.475	-0.3118	2.881	0.0777	0.011	-0.2241	0.0427	-0.0604	0.251	0.0948	-0.1745	-0.0172	0.0994	-0.0274	0.0053	0.0387	0.0103	0.1175	-18.111	-15.9981	-35.7786
10	0.582	0.4928	-1.1762	4.3649	-0.1132	2.5942	-0.0483	-0.0643	-0.096	-0.0121	-0.0842	-0.2075	0.0648	0.0999	0.1325	0.1067	0.0154	-0.021	0.0487	0.0715	0.1494	2.7997	-28.0589	-37.3365
11	1.9603	-0.3644	-1.1545	2.292	0.4056	1.4808	0.0159	0.2005	-0.19	-0.034	-0.0431	-0.1028	0.1026	-0.0629	0.0272	0.0843	-0.0026	-0.0241	0.0431	0.0078	0.0899	-1.3135	-24.2566	-41.8698
12	5.5606	1.5327	-0.7658	3.0388	0.0382	0.7583	0.0681	-0.0808	0.1669	0.1291	-0.0858	-0.0999	-0.0133	0.0129	0.0177	0.0679	-0.0091	-0.0172	0.011	0.0221	0.0685	-0.73	-15.015	-41.0718
13	1.1161	-0.0018	-0.067	2.3437	-0.3596	1.4853	0.0988	0.237	-0.0387	-0.2402	-0.1355	0.0524	-0.0243	0.0031	0.0367	0.1076	0.0143	-0.0114	0.0789	0.0156	0.0518	-6.6244	-11.59	-49.5616
14	1.1094	0.0884	0.2191	1.033	0.5829	2.2923	-0.0075	-0.0214	0.0319	-0.0281	-0.0014	-0.0028	-0.0697	0.0906	0.009	0.0759	-0.0173	0.003	0.023	0.0301	0.0656	-6.8769	-0.7927	-31.2807
15	0.2688	-0.6073	0.2755	2.861	-0.3046	2.7453	0.0103	0.0022	-0.0153	0.0665	-0.0035	-0.1157	0.2245	0.1055	-0.0068	0.1482	-0.0198	0.0078	0.0291	0.0291	0.07	-6.9577	-14.9876	-23.1964
16	14.6169	-4.0541	8.1626	9.2393	-4.2326	20.121	0.2191	-1.0182	0.065	0.4901	0.0571	0.6254	0.2196	-1.3109	-0.2762	0.1509	-0.052	0.0667	0.1568	0.028	0.1117	-17.0422	-14.9762	-15.6473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-8 - 13
2	X-RAY DIFFRACTION	2	A	14 - 34
3	X-RAY DIFFRACTION	3	A	35 - 44
4	X-RAY DIFFRACTION	4	A	45 - 90
5	X-RAY DIFFRACTION	5	A	91 - 140
6	X-RAY DIFFRACTION	6	A	141 - 192
7	X-RAY DIFFRACTION	7	A	193 - 213
8	X-RAY DIFFRACTION	8	A	214 - 251
9	X-RAY DIFFRACTION	9	B	-8 - 20
10	X-RAY DIFFRACTION	10	B	21 - 38
11	X-RAY DIFFRACTION	11	B	39 - 73
12	X-RAY DIFFRACTION	12	B	74 - 90
13	X-RAY DIFFRACTION	13	B	91 - 139
14	X-RAY DIFFRACTION	14	B	140 - 212
15	X-RAY DIFFRACTION	15	B	213 - 247
16	X-RAY DIFFRACTION	16	B	248 - 252

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