PDB-5b6p: Structure of the dodecameric type-II dehydrogenate dehydratase fr...

Basic information

• Entry: Database: PDB / ID: 5b6p
• Title: Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution
• Components: 3-dehydroquinate dehydratase
• Keywords: LYASE

Function / homology

Function:

quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process

Domain/homology:

Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

3-dehydroquinate dehydratase

• Biological species: Acinetobacter baumannii (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
• Authors: Kumar, M. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
• Citation: Journal: Int. J. Biol. Macromol. / Year: 2017; Title: Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii.; Authors: Iqbal, N. / Kumar, M. / Sharma, P. / Yadav, S.P. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	May 31, 2016	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Sep 7, 2016	ID: 5IBA
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Derived calculations Category: citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Assembly

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

hetero molecules

Summary:

• 199 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	199,354	24
Polymers	198,202	12
Non-polymers	1,153	12
Water	13,854	769

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	29380 Å2
ΔGint	-337 kcal/mol
Surface area	63480 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	82.284, 95.279, 132.263
Angle α, β, γ (deg.)	90.00, 95.73, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 3 - 147 / Label seq-ID: 3 - 147

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase

Details:

Mass: 16516.803 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Gene: aroQ, A1S_2009 / Plasmid: pET-28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3M692, 3-dehydroquinate dehydratase

#2: Chemical

A-201 B-201 C-201 D-201 E-201 F-201 G-201 H-201 I-201 J-201 K-201 L-201
ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.6 ų/Da / Density % sol: 53 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 ; Details: 30% PEG 3350, MgSO4, Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Data collection

• Diffraction: Mean temperature: 77 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
• Detector: Type: MARRESEARCH / Detector: CCD / Date: Apr 8, 2014 / Details: Mirror
• Radiation: Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97 Å / Relative weight: 1
• Reflection: Resolution: 2→131.6 Å / Num. obs: 129427 / % possible obs: 96.2 % / Redundancy: 7.6 % / B_iso Wilson estimate: 22.8 Ų / R_sym value: 0.09 / Net I/av σ(I): 31 / Net I/σ(I): 31
• Reflection shell: Resolution: 2→2.03 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.441 / Mean I/σ(I) obs: 4.6 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.8.0123	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWZ

3lwz

Resolution: 2→131.6 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.927 / SU B: 4.149 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.23215	1588	1.2 %	RANDOM
Rwork	0.20059	-	-	-
obs	0.20098	129427	96.2 %	-

• 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: 29.142 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.63 Å2	-0 Å2	-0.09 Å2
2-	-	0.09 Å2	-0 Å2
3-	-	-	-0.69 Å2

Refinement step

Cycle: LAST / Resolution: 2→131.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13452	0	60	769	14281

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	13763
X-RAY DIFFRACTION	r_bond_other_d	0.016	0.02	13488
X-RAY DIFFRACTION	r_angle_refined_deg	1.909	1.951	18729
X-RAY DIFFRACTION	r_angle_other_deg	2.482	3	30851
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.262	5	1727
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.781	24.314	612
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.775	15	2268
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.453	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	2220
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	15605
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	3179
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	3.052	2.667	6947
X-RAY DIFFRACTION	r_mcbond_other	3.047	2.667	6946
X-RAY DIFFRACTION	r_mcangle_it	4.625	3.977	8661
X-RAY DIFFRACTION	r_mcangle_other	4.625	3.978	8662
X-RAY DIFFRACTION	r_scbond_it	3.563	3.132	6816
X-RAY DIFFRACTION	r_scbond_other	3.56	3.133	6813
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.547	4.555	10063
X-RAY DIFFRACTION	r_long_range_B_refined	7.812	22.433	15814
X-RAY DIFFRACTION	r_long_range_B_other	7.811	22.428	15803
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	17700	0.1
1	2	B	17700	0.1
2	1	A	17560	0.11
2	2	C	17560	0.11
3	1	A	17746	0.11
3	2	D	17746	0.11
4	1	A	17638	0.11
4	2	E	17638	0.11
5	1	A	17992	0.11
5	2	F	17992	0.11
6	1	A	17764	0.1
6	2	G	17764	0.1
7	1	A	17572	0.11
7	2	H	17572	0.11
8	1	A	17512	0.1
8	2	I	17512	0.1
9	1	A	17410	0.12
9	2	J	17410	0.12
10	1	A	17770	0.11
10	2	K	17770	0.11
11	1	A	17576	0.1
11	2	L	17576	0.1
12	1	B	17530	0.11
12	2	C	17530	0.11
13	1	B	17492	0.1
13	2	D	17492	0.1
14	1	B	17804	0.1
14	2	E	17804	0.1
15	1	B	17726	0.11
15	2	F	17726	0.11
16	1	B	17650	0.1
16	2	G	17650	0.1
17	1	B	17592	0.1
17	2	H	17592	0.1
18	1	B	17610	0.1
18	2	I	17610	0.1
19	1	B	17568	0.11
19	2	J	17568	0.11
20	1	B	17892	0.1
20	2	K	17892	0.1
21	1	B	17584	0.1
21	2	L	17584	0.1
22	1	C	17378	0.11
22	2	D	17378	0.11
23	1	C	17554	0.11
23	2	E	17554	0.11
24	1	C	17716	0.11
24	2	F	17716	0.11
25	1	C	17454	0.12
25	2	G	17454	0.12
26	1	C	17338	0.12
26	2	H	17338	0.12
27	1	C	17466	0.12
27	2	I	17466	0.12
28	1	C	17372	0.13
28	2	J	17372	0.13
29	1	C	17504	0.12
29	2	K	17504	0.12
30	1	C	17660	0.11
30	2	L	17660	0.11
31	1	D	17674	0.1
31	2	E	17674	0.1
32	1	D	17866	0.1
32	2	F	17866	0.1
33	1	D	17842	0.09
33	2	G	17842	0.09
34	1	D	17852	0.09
34	2	H	17852	0.09
35	1	D	17468	0.11
35	2	I	17468	0.11
36	1	D	17258	0.12
36	2	J	17258	0.12
37	1	D	17678	0.11
37	2	K	17678	0.11
38	1	D	17808	0.09
38	2	L	17808	0.09
39	1	E	17790	0.11
39	2	F	17790	0.11
40	1	E	17594	0.11
40	2	G	17594	0.11
41	1	E	17730	0.1
41	2	H	17730	0.1
42	1	E	17630	0.1
42	2	I	17630	0.1
43	1	E	17546	0.12
43	2	J	17546	0.12
44	1	E	17944	0.1
44	2	K	17944	0.1
45	1	E	17746	0.1
45	2	L	17746	0.1
46	1	F	17774	0.1
46	2	G	17774	0.1
47	1	F	17786	0.1
47	2	H	17786	0.1
48	1	F	17520	0.11
48	2	I	17520	0.11
49	1	F	17466	0.12
49	2	J	17466	0.12
50	1	F	17916	0.1
50	2	K	17916	0.1
51	1	F	17830	0.1
51	2	L	17830	0.1
52	1	G	17944	0.09
52	2	H	17944	0.09
53	1	G	17850	0.1
53	2	I	17850	0.1
54	1	G	17676	0.12
54	2	J	17676	0.12
55	1	G	17750	0.1
55	2	K	17750	0.1
56	1	G	17926	0.09
56	2	L	17926	0.09
57	1	H	17572	0.1
57	2	I	17572	0.1
58	1	H	17336	0.12
58	2	J	17336	0.12
59	1	H	17594	0.11
59	2	K	17594	0.11
60	1	H	17838	0.09
60	2	L	17838	0.09
61	1	I	17518	0.12
61	2	J	17518	0.12
62	1	I	17764	0.1
62	2	K	17764	0.1
63	1	I	17876	0.1
63	2	L	17876	0.1
64	1	J	17702	0.11
64	2	K	17702	0.11
65	1	J	17602	0.12
65	2	L	17602	0.12
66	1	K	17680	0.1
66	2	L	17680	0.1

LS refinement shell

Resolution: 2.005→2.057 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.309	108	-
Rwork	0.205	9595	-
obs	-	-	97.11 %