PDB-5x47: Crystal structure of dehydroquinate dehydratase from Acinetobacte...

ID or keywords:

Entry

Database: PDB / ID: 5x47

Title

Crystal structure of dehydroquinate dehydratase from Acinetobacter baumannii at 2.5 Angstrom resolution

Components

3-dehydroquinate dehydratase

Keywords

LYASE

Function / homology

Function and homology information

quinate catabolic 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

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.54 Å

Authors

Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.

Citation

Journal: To Be Published
Title: Crystal structure of dehydroquinate dehydratase from Acinetobacter baumannii at 2.5 Angstrom resolution
Authors: Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	Feb 10, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5x47.cif.gz	672 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5x47_validation.pdf.gz	524 KB	Display	wwPDB validaton report
Full document	5x47_full_validation.pdf.gz	584.7 KB	Display
Data in XML	5x47_validation.xml.gz	62.9 KB	Display
Data in CIF	5x47_validation.cif.gz	85.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/5x47 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x47	HTTPS FTP

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Related structure data

Related structure data	5wrfS S: Starting model for refinement
Similar structure data	5yl5-d 5ypq-d 4zc1-d 5wrf-d 5yhm-d 4rhc-d 5b6p-d 1gu0-d 6hsb-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

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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 (6)

Deposited unit

A: 3-dehydroquinate dehydratase

B: 3-dehydroquinate dehydratase

C: 3-dehydroquinate dehydratase

D: 3-dehydroquinate dehydratase

E: 3-dehydroquinate dehydratase

F: 3-dehydroquinate dehydratase

G: 3-dehydroquinate dehydratase

H: 3-dehydroquinate dehydratase

I: 3-dehydroquinate dehydratase

J: 3-dehydroquinate dehydratase

K: 3-dehydroquinate dehydratase

L: 3-dehydroquinate dehydratase

191 kDa, 12 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)	97.993, 136.254, 143.209
Angle α, β, γ (deg.)	90.00, 97.59, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 2 - 146 / Label seq-ID: 1 - 145

NCS ensembles :

#1: Protein	3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase Mass: 15876.093 Da / Num. of mol.: 12 / Fragment: UNP residues 2-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 Gene: aroQ, A1S_2009 / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692, 3-dehydroquinate dehydratase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.49 Å³/Da / Density % sol: 50.55 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350, MgSO4, Tris buffer

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.54→49.15 Å / Num. obs: 61621 / % possible obs: 69.4 % / Redundancy: 2.55 % / R_sym value: 0.168 / Net I/σ(I): 7.18
Reflection shell	Resolution: 2.54→2.59 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 61621 / R_sym value: 0.383 / % possible all: 92

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WRF

5wrf

Resolution: 2.54→47.932 Å / Cor.coef. F_o:F_c: 0.879 / Cor.coef. F_o:F_c free: 0.806 / SU B: 59.369 / SU ML: 0.519 / Cross valid method: THROUGHOUT / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30524	2142	4.9 %	RANDOM
R_work	0.2526	-	-	-
obs	0.25521	41209	70.32 %	-

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: 51.292 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.65 Å²	0 Å²	-1.17 Å²
2-	-	-5.55 Å²	0 Å²
3-	-	-	3.1 Å²

Refinement step

Cycle: 1 / Resolution: 2.54→47.932 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13440	0	0	38	13478

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.019	13692
X-RAY DIFFRACTION	r_bond_other_d	0.048	0.02	13452
X-RAY DIFFRACTION	r_angle_refined_deg	2.12	1.944	18611
X-RAY DIFFRACTION	r_angle_other_deg	4.835	3	30756
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.091	5	1728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.332	24.314	612
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.112	15	2280
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.258	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.147	0.2	2208
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	15596
X-RAY DIFFRACTION	r_gen_planes_other	0.028	0.02	3192
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	5.042	2.589	6948
X-RAY DIFFRACTION	r_mcbond_other	5.042	2.588	6947
X-RAY DIFFRACTION	r_mcangle_it	6.706	3.864	8664
X-RAY DIFFRACTION	r_mcangle_other	6.706	3.865	8665
X-RAY DIFFRACTION	r_scbond_it	5.817	2.912	6744
X-RAY DIFFRACTION	r_scbond_other	5.817	2.912	6745
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.504	4.247	9948
X-RAY DIFFRACTION	r_long_range_B_refined	8.706	23.717	57783
X-RAY DIFFRACTION	r_long_range_B_other	8.68	23.712	57781
X-RAY DIFFRACTION	r_rigid_bond_restr	16.51	3	27144
X-RAY DIFFRACTION	r_sphericity_free	78.165	5	15
X-RAY DIFFRACTION	r_sphericity_bonded	20.978	5	26917

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	17022	0.15
1	2	B	17022	0.15
2	1	A	16774	0.14
2	2	C	16774	0.14
3	1	A	16036	0.17
3	2	D	16036	0.17
4	1	A	16570	0.15
4	2	E	16570	0.15
5	1	A	16306	0.16
5	2	F	16306	0.16
6	1	A	16366	0.16
6	2	G	16366	0.16
7	1	A	16372	0.16
7	2	H	16372	0.16
8	1	A	16138	0.17
8	2	I	16138	0.17
9	1	A	16052	0.17
9	2	J	16052	0.17
10	1	A	16326	0.16
10	2	K	16326	0.16
11	1	A	15868	0.18
11	2	L	15868	0.18
12	1	B	16830	0.14
12	2	C	16830	0.14
13	1	B	16030	0.17
13	2	D	16030	0.17
14	1	B	16798	0.15
14	2	E	16798	0.15
15	1	B	16402	0.15
15	2	F	16402	0.15
16	1	B	16516	0.15
16	2	G	16516	0.15
17	1	B	16366	0.16
17	2	H	16366	0.16
18	1	B	16312	0.16
18	2	I	16312	0.16
19	1	B	16202	0.17
19	2	J	16202	0.17
20	1	B	16404	0.15
20	2	K	16404	0.15
21	1	B	15868	0.18
21	2	L	15868	0.18
22	1	C	16528	0.16
22	2	D	16528	0.16
23	1	C	17004	0.14
23	2	E	17004	0.14
24	1	C	16892	0.14
24	2	F	16892	0.14
25	1	C	16884	0.15
25	2	G	16884	0.15
26	1	C	16954	0.15
26	2	H	16954	0.15
27	1	C	16616	0.15
27	2	I	16616	0.15
28	1	C	16390	0.17
28	2	J	16390	0.17
29	1	C	16906	0.14
29	2	K	16906	0.14
30	1	C	16364	0.17
30	2	L	16364	0.17
31	1	D	16364	0.17
31	2	E	16364	0.17
32	1	D	16424	0.17
32	2	F	16424	0.17
33	1	D	16340	0.17
33	2	G	16340	0.17
34	1	D	16348	0.17
34	2	H	16348	0.17
35	1	D	16150	0.18
35	2	I	16150	0.18
36	1	D	15956	0.18
36	2	J	15956	0.18
37	1	D	16340	0.17
37	2	K	16340	0.17
38	1	D	16050	0.19
38	2	L	16050	0.19
39	1	E	16678	0.15
39	2	F	16678	0.15
40	1	E	16874	0.15
40	2	G	16874	0.15
41	1	E	16906	0.15
41	2	H	16906	0.15
42	1	E	16722	0.16
42	2	I	16722	0.16
43	1	E	16568	0.16
43	2	J	16568	0.16
44	1	E	16818	0.14
44	2	K	16818	0.14
45	1	E	16328	0.17
45	2	L	16328	0.17
46	1	F	16426	0.15
46	2	G	16426	0.15
47	1	F	16540	0.14
47	2	H	16540	0.14
48	1	F	16268	0.16
48	2	I	16268	0.16
49	1	F	15974	0.17
49	2	J	15974	0.17
50	1	F	16720	0.14
50	2	K	16720	0.14
51	1	F	16318	0.16
51	2	L	16318	0.16
52	1	G	16766	0.16
52	2	H	16766	0.16
53	1	G	16444	0.17
53	2	I	16444	0.17
54	1	G	16130	0.17
54	2	J	16130	0.17
55	1	G	16734	0.15
55	2	K	16734	0.15
56	1	G	16050	0.18
56	2	L	16050	0.18
57	1	H	16564	0.17
57	2	I	16564	0.17
58	1	H	16326	0.17
58	2	J	16326	0.17
59	1	H	16672	0.15
59	2	K	16672	0.15
60	1	H	16288	0.17
60	2	L	16288	0.17
61	1	I	16110	0.18
61	2	J	16110	0.18
62	1	I	16438	0.16
62	2	K	16438	0.16
63	1	I	16208	0.17
63	2	L	16208	0.17
64	1	J	16282	0.17
64	2	K	16282	0.17
65	1	J	15776	0.19
65	2	L	15776	0.19
66	1	K	16260	0.17
66	2	L	16260	0.17

LS refinement shell

Resolution: 2.537→2.602 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.582	16	-
R_work	0.406	353	-
obs	-	-	8.16 %

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	0.2879	-0.0813	-0.0673	0.2793	-0.3139	0.4485	-0.0083	0.015	0.018	-0.0409	-0.0112	-0.0323	0.0566	0.0133	0.0195	0.012	0.0037	0.0496	0.3788	0.0013	0.4551	-36.384	16.6917	7.9763
2	0.2254	0.1885	0.1354	0.3652	-0.1044	0.3811	-0.0602	-0.0142	0.0119	-0.0997	0.038	-0.0124	-0.0123	-0.0218	0.0221	0.043	-0.0014	0.0555	0.3848	-0.0136	0.4534	-56.2055	-3.0559	20.6785
3	0.4164	0.0013	-0.078	0.0607	-0.1335	0.3763	0.049	0.051	-0.0237	0.0128	-0.0285	0.0051	-0.017	-0.0087	-0.0205	0.0238	0.0033	0.0543	0.3664	0.0015	0.4557	-31.9353	-13.5848	5.131
4	0.3958	-0.1208	-0.1649	0.6167	-0.3017	0.4428	-0.0564	-0.0499	0.0288	0.0505	0.0205	0.0423	-0.0281	0.0365	0.0359	0.0215	-0.027	0.0199	0.3375	-0.0158	0.4328	-22.7872	30.5728	23.3271
5	0.6987	0.1587	0.1853	0.3185	-0.2141	0.2874	-0.0653	-0.057	-0.0033	-0.0421	0.0058	-0.0459	0.0127	0.0072	0.0595	0.0173	0.0114	0.0638	0.3802	-0.0216	0.417	5.4665	-6.9468	36.1674
6	0.4395	0.0541	-0.2714	0.6837	-0.0334	0.6538	0.0439	-0.0076	-0.0147	-0.038	-0.0517	-0.0174	-0.0269	0.0178	0.0077	0.0136	0.0049	0.0533	0.3578	0.006	0.4414	-11.9269	-23.1948	16.6904
7	0.3418	-0.0241	0.1119	0.0841	-0.2795	1.0415	-0.0953	-0.0277	-0.115	-0.0324	0.0819	-0.0147	0.1158	-0.1056	0.0134	0.0534	0.0105	0.0852	0.3987	0.0383	0.4012	-14.0157	-27.9794	47.0866
8	0.1212	-0.1275	0.0959	0.9655	-0.0351	0.0853	-0.0625	-0.0137	0.028	-0.0569	0.0372	-0.1485	-0.0585	-0.0476	0.0254	0.0529	-0.0015	0.0303	0.3746	-0.009	0.4938	1.3869	17.2749	37.3847
9	0.6187	0.4049	0.1549	0.3618	0.1405	0.0556	0.0243	-0.1268	0.092	-0.049	-0.0576	0.0778	-0.023	-0.0437	0.0333	0.0642	0.0339	0.0736	0.4423	-0.0156	0.3849	-39.3529	10.4865	63.3952
10	0.6818	-0.1937	0.3035	0.6388	0.2611	0.3548	-0.0799	-0.1562	-0.06	0.0929	0.0829	-0.0447	0.0143	-0.0957	-0.003	0.0356	0.0226	0.0831	0.4605	0.0436	0.4249	-32.9856	-19.7724	60.58
11	0.3823	-0.1621	-0.0927	0.4038	0.084	0.0296	-0.0951	-0.106	0.0226	0.0077	0.09	-0.0558	0.0218	0.0186	0.0051	0.0361	0.0012	0.0566	0.4372	0.0016	0.4173	-56.7506	-7.5124	45.2496
12	0.036	0.0257	0.0172	0.0374	0.0207	0.0126	-0.0055	-0.095	0.0513	0.0161	-0.0199	0.0567	0.0089	-0.0291	0.0254	0.0481	0.039	0.031	0.407	-0.0448	0.3892	-22.9563	26.4436	54.1325

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 146
2	X-RAY DIFFRACTION	2	B	2 - 146
3	X-RAY DIFFRACTION	3	C	2 - 146
4	X-RAY DIFFRACTION	4	D	2 - 146
5	X-RAY DIFFRACTION	5	E	2 - 146
6	X-RAY DIFFRACTION	6	F	2 - 146
7	X-RAY DIFFRACTION	7	G	2 - 146
8	X-RAY DIFFRACTION	8	H	2 - 146
9	X-RAY DIFFRACTION	9	I	2 - 146
10	X-RAY DIFFRACTION	10	J	2 - 146
11	X-RAY DIFFRACTION	11	K	2 - 146
12	X-RAY DIFFRACTION	12	L	2 - 146

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