PDB-5wrf: Crystal structure of dodecameric type II dehydroquinate dehydrata...

Basic information

• Entry: Database: PDB / ID: 5wrf
• Title: Crystal structure of dodecameric type II dehydroquinate dehydratase from Acinetobacter baumannii with unexplained connecting electron density between free cysteine residues of molecular pairs
• 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: 2.51 Å
• Authors: Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
• Citation: Journal: To Be Published; Title: Crystal structure of dodecameric type II dehydroquinate dehydratase from Acinetobacter baumannii with unexplained connecting electron density between free cysteine residues of molecular pairs; Authors: Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	Dec 1, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 21, 2016	Provider: repository / Type: Initial release
Revision 1.1	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:

• 191 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	190,575	13
Polymers	190,513	12
Non-polymers	62	1
Water	3,621	201

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	26890 Å2
ΔGint	-118 kcal/mol
Surface area	65250 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	97.801, 135.750, 142.740
Angle α, β, γ (deg.)	90.00, 97.53, 90.00
Int Tables number	5
Space group name H-M	C121

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

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: 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: Chemical

A-201 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.47 ų/Da / Density % sol: 50.11 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350, MgSO4, Tris buffer

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: Sep 22, 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: 2.51→37.75 Å / Num. obs: 63061 / % possible obs: 95.3 % / Redundancy: 3.5 % / R_sym value: 0.084 / Net I/σ(I): 13.4
• Reflection shell: Resolution: 2.51→2.54 Å / % possible all: 94.6

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: 4RHC

4rhc

Resolution: 2.51→37.75 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.916 / SU B: 11.686 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.999 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.25588	1159	1.9 %	RANDOM
Rwork	0.20915	-	-	-
obs	0.21002	58540	94.67 %	-

• 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: 54.63 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-2.35 Å2	0 Å2	-0.73 Å2
2-	-	1.71 Å2	0 Å2
3-	-	-	0.81 Å2

Refinement step

Cycle: 1 / Resolution: 2.51→37.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13440	0	4	201	13645

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	13695
X-RAY DIFFRACTION	r_bond_other_d	0.028	0.02	13457
X-RAY DIFFRACTION	r_angle_refined_deg	2.094	1.944	18613
X-RAY DIFFRACTION	r_angle_other_deg	3.438	3	30767
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.266	5	1728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.427	24.314	612
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.174	15	2280
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.463	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.134	0.2	2208
X-RAY DIFFRACTION	r_gen_planes_refined	0.02	0.02	15596
X-RAY DIFFRACTION	r_gen_planes_other	0.022	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	4.307	5.316	6948
X-RAY DIFFRACTION	r_mcbond_other	4.305	5.315	6947
X-RAY DIFFRACTION	r_mcangle_it	6.744	7.95	8664
X-RAY DIFFRACTION	r_mcangle_other	6.744	7.951	8665
X-RAY DIFFRACTION	r_scbond_it	4.171	5.689	6747
X-RAY DIFFRACTION	r_scbond_other	4.171	5.689	6747
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.569	8.391	9950
X-RAY DIFFRACTION	r_long_range_B_refined	11.094	49.294	56433
X-RAY DIFFRACTION	r_long_range_B_other	11.094	49.293	56434
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	17118	0.13
1	2	B	17118	0.13
2	1	A	16818	0.13
2	2	C	16818	0.13
3	1	A	16212	0.15
3	2	D	16212	0.15
4	1	A	16644	0.14
4	2	E	16644	0.14
5	1	A	16500	0.14
5	2	F	16500	0.14
6	1	A	16686	0.14
6	2	G	16686	0.14
7	1	A	16476	0.15
7	2	H	16476	0.15
8	1	A	16372	0.15
8	2	I	16372	0.15
9	1	A	16122	0.16
9	2	J	16122	0.16
10	1	A	16210	0.15
10	2	K	16210	0.15
11	1	A	15930	0.16
11	2	L	15930	0.16
12	1	B	16946	0.13
12	2	C	16946	0.13
13	1	B	16266	0.15
13	2	D	16266	0.15
14	1	B	16832	0.14
14	2	E	16832	0.14
15	1	B	16638	0.13
15	2	F	16638	0.13
16	1	B	16802	0.14
16	2	G	16802	0.14
17	1	B	16618	0.14
17	2	H	16618	0.14
18	1	B	16540	0.14
18	2	I	16540	0.14
19	1	B	16192	0.15
19	2	J	16192	0.15
20	1	B	16382	0.15
20	2	K	16382	0.15
21	1	B	15984	0.15
21	2	L	15984	0.15
22	1	C	16806	0.13
22	2	D	16806	0.13
23	1	C	17136	0.13
23	2	E	17136	0.13
24	1	C	17124	0.12
24	2	F	17124	0.12
25	1	C	17180	0.12
25	2	G	17180	0.12
26	1	C	17004	0.14
26	2	H	17004	0.14
27	1	C	16744	0.13
27	2	I	16744	0.13
28	1	C	16632	0.14
28	2	J	16632	0.14
29	1	C	16714	0.14
29	2	K	16714	0.14
30	1	C	16568	0.15
30	2	L	16568	0.15
31	1	D	16646	0.14
31	2	E	16646	0.14
32	1	D	16812	0.14
32	2	F	16812	0.14
33	1	D	16730	0.13
33	2	G	16730	0.13
34	1	D	16414	0.15
34	2	H	16414	0.15
35	1	D	16314	0.15
35	2	I	16314	0.15
36	1	D	16212	0.15
36	2	J	16212	0.15
37	1	D	16294	0.15
37	2	K	16294	0.15
38	1	D	16220	0.15
38	2	L	16220	0.15
39	1	E	17094	0.12
39	2	F	17094	0.12
40	1	E	17266	0.12
40	2	G	17266	0.12
41	1	E	17236	0.13
41	2	H	17236	0.13
42	1	E	17076	0.13
42	2	I	17076	0.13
43	1	E	16638	0.15
43	2	J	16638	0.15
44	1	E	16800	0.14
44	2	K	16800	0.14
45	1	E	16612	0.14
45	2	L	16612	0.14
46	1	F	16966	0.13
46	2	G	16966	0.13
47	1	F	16696	0.13
47	2	H	16696	0.13
48	1	F	16464	0.13
48	2	I	16464	0.13
49	1	F	16256	0.15
49	2	J	16256	0.15
50	1	F	16678	0.14
50	2	K	16678	0.14
51	1	F	16582	0.14
51	2	L	16582	0.14
52	1	G	16876	0.14
52	2	H	16876	0.14
53	1	G	16872	0.14
53	2	I	16872	0.14
54	1	G	16474	0.15
54	2	J	16474	0.15
55	1	G	16546	0.14
55	2	K	16546	0.14
56	1	G	16468	0.14
56	2	L	16468	0.14
57	1	H	16826	0.13
57	2	I	16826	0.13
58	1	H	16532	0.15
58	2	J	16532	0.15
59	1	H	16614	0.15
59	2	K	16614	0.15
60	1	H	16446	0.15
60	2	L	16446	0.15
61	1	I	16372	0.15
61	2	J	16372	0.15
62	1	I	16416	0.15
62	2	K	16416	0.15
63	1	I	16360	0.15
63	2	L	16360	0.15
64	1	J	16214	0.16
64	2	K	16214	0.16
65	1	J	16032	0.17
65	2	L	16032	0.17
66	1	K	16190	0.16
66	2	L	16190	0.16

LS refinement shell

Resolution: 2.51→2.575 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.322	79	-
Rwork	0.295	3918	-
obs	-	-	86.72 %