PDB-2c57: H.pylori type II dehydroquinase in complex with FA1

ID or keywords:

Entry

Database: PDB / ID: 2c57

Title

H.pylori type II dehydroquinase in complex with FA1

Components

3-DEHYDROQUINATE DEHYDRATASE

Keywords

LYASE / DEHYDROQUINASE / DEHYDROQUINATE / SULPHONAMIDE / 3-DEHYDROQUINASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS

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

HELICOBACTER PYLORI (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Robinson, D.A. / Lapthorn, A.J.

Citation

Journal: J.Med.Chem. / Year: 2006
Title: Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design.
Authors: Robinson, D.A. / Stewart, K.A. / Price, N.C. / Chalk, P.A. / Coggins, J.R. / Lapthorn, A.J.

History

Deposition	Oct 26, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2c57.cif.gz	346.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2c57.ent.gz	282.5 KB	Display	PDB format
PDBx/mmJSON format	2c57.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2c57_validation.pdf.gz	352.8 KB	Display	wwPDB validaton report
Full document	2c57_full_validation.pdf.gz	362.1 KB	Display
Data in XML	2c57_validation.xml.gz	37.7 KB	Display
Data in CIF	2c57_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/2c57 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c57	HTTPS FTP

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Related structure data

Related structure data	2c4vC 2c4wSC 1j2y C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1j2y-1 1ylv-1 2xb9-1 4b6s-1 1h7r-1 1ohl-1 1gjp-1 1h7n-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 (7)

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

242 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)	103.863, 103.863, 217.531
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	C
3	1	E
4	1	F
5	1	H
6	1	I
7	1	K
8	1	L
1	2	A
2	2	D
3	2	G
4	2	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	B	1 - 200
2	1	1	1	C	1 - 200
3	1	1	1	E	1 - 200
4	1	1	1	F	1 - 200
5	1	1	1	H	1 - 200
6	1	1	1	I	1 - 200
7	1	1	1	K	1 - 200
8	1	1	1	L	1 - 200
1	1	2	1	A	-18 - 200
2	1	2	1	D	-18 - 200
3	1	2	1	G	-18 - 200
4	1	2	1	J	-18 - 200

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.00779, 0.00496, -0.99996), (-0.99961, -0.02694, -0.00792), (-0.02698, 0.99962, 0.00474)	88.50494, 30.85147, 58.6063
2	given	(-0.00233, -0.99998, -0.00507), (0.02647, -0.00513, 0.99964), (-0.99965, 0.00219, 0.02649)	30.48246, -59.01868, 86.67141
3	given	(1, -0.00066, -0.00087), (-0.00066, -1, -0.00024), (-0.00087, 0.00024, -1)	0.11995, 60.00494, 176.90218
4	given	(0.00936, -0.00508, 0.99994), (-0.99958, 0.02724, 0.00949), (-0.02729, -0.99962, -0.00482)	-88.12927, 27.68261, 119.37479
5	given	(-0.00308, 0.99998, 0.00481), (0.02682, 0.00489, -0.99963), (-0.99964, -0.00295, -0.02684)	-30.3249, 117.54192, 91.55891
6	given	(-1, -0.00111, -6.0E-5), (0.00111, -1, 0.0002), (-6.0E-5, 0.0002, 1)	0.0481, 59.95547, -0.00703
7	given	(-0.00676, -0.00584, -0.99996), (0.99963, 0.02637, -0.00691), (0.02641, -0.99964, 0.00566)	88.86494, 29.19655, 118.47969
8	given	(0.00312, 0.99998, -0.00632), (-0.02546, 0.0064, 0.99966), (0.99967, -0.00296, 0.02548)	-29.34498, -59.35654, 86.91813
9	given	(-1, 0.00081, -0.00149), (0.00081, 1, -0.00046), (0.00149, -0.00046, -1)	0.15021, 0.05734, 176.93422
10	given	(-0.00789, 0.00445, 0.99996), (0.99963, -0.02602, 0.00801), (0.02605, 0.99965, -0.00424)	-88.42444, 29.44497, 59.38031
11	given	(0.00327, -0.99998, 0.00525), (-0.0262, -0.00533, -0.99964), (0.99965, 0.00313, -0.02622)	29.61763, 117.87177, 91.31122

#1: Protein	3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE Mass: 19958.715 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical	ChemComp-FA1 / 2,3 -ANHYDRO-QUINIC ACID Mass: 174.151 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₇H₁₀O₅
Compound details	CATALYZES A TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.37 Å³/Da / Density % sol: 63.19 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 8.8 Details: 10MG/ML PROTEIN AGAINST 30% 1,4 BUTANDIOL, 0.1M SODIUM ACETATE PH 4.5 USING SITTING DROP METHOD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 5, 2002 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.08→46.6 Å / Num. obs: 43781 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / B_iso Wilson estimate: 78 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 3 % / R_merge(I) obs: 0.85 / Mean I/σ(I) obs: 1.2 / % possible all: 81.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C4W

2c4w

Resolution: 3.1→25 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.903 / SU B: 45.975 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	3968	10 %	RANDOM
R_work	0.207	-	-	-
obs	0.21	35869	83.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 61.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.05 Å²	0.52 Å²	0 Å²
2-	-	1.05 Å²	0 Å²
3-	-	-	-1.57 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14224	0	144	0	14368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	14584
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.076	1.954	19684
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.733	5	1852
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.766	26.325	664
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.972	15	2484
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.844	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	2248
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10936
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.264	0.2	7740
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.338	0.2	10022
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	661
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	0.234	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.529	0.2	4
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	0.317	1.5	9482
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.421	2	14728
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.611	3	5591
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.786	4.5	4956
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	B	1165	tight positional	0.06	0.05
1	2	C	1165	tight positional	0.06	0.05
1	3	E	1165	tight positional	0.06	0.05
1	4	F	1165	tight positional	0.06	0.05
1	5	H	1165	tight positional	0.06	0.05
1	6	I	1165	tight positional	0.06	0.05
1	7	K	1165	tight positional	0.06	0.05
1	8	L	1165	tight positional	0.06	0.05
2	1	A	1262	tight positional	0.05	0.05
2	2	D	1262	tight positional	0.05	0.05
2	3	G	1262	tight positional	0.05	0.05
2	4	J	1262	tight positional	0.05	0.05
1	1	B	1165	tight thermal	0.11	0.5
1	2	C	1165	tight thermal	0.11	0.5
1	3	E	1165	tight thermal	0.11	0.5
1	4	F	1165	tight thermal	0.11	0.5
1	5	H	1165	tight thermal	0.13	0.5
1	6	I	1165	tight thermal	0.11	0.5
1	7	K	1165	tight thermal	0.12	0.5
1	8	L	1165	tight thermal	0.11	0.5
2	1	A	1262	tight thermal	0.12	0.5
2	2	D	1262	tight thermal	0.12	0.5
2	3	G	1262	tight thermal	0.11	0.5
2	4	J	1262	tight thermal	0.11	0.5

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.368	236
R_work	0.384	2018

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	4.5454	-0.6991	0.2976	4.7248	-0.6306	6.7283	0.4586	0.4792	0.2632	-1.0605	-0.1107	-0.3536	-0.0213	0.2844	-0.348	-0.1283	0.2779	0.0595	-0.4567	-0.1285	-0.2872	10.2602	23.4222	56.0674
2	5.6535	0.6029	-1.4354	6.0775	0.1248	5.7843	0.0227	0.222	-0.6082	-0.0904	0.0982	0.0388	1.2693	0.0377	-0.1209	0.1138	0.168	-0.2422	-0.4713	-0.0804	-0.396	6.481	-1.509	78.9261
3	5.3379	0.3926	0.8476	5.6636	0.3577	6.142	0.24	-0.1841	0.0284	-0.1752	0.2359	-1.3178	0.4582	1.3414	-0.4759	-0.4456	0.2279	0.0172	0.0759	-0.3738	0.1038	31.6034	20.3697	82.1131
4	4.3207	0.7421	-0.3726	4.3919	-0.3944	6.7085	0.4001	-0.5094	-0.3048	1.0333	-0.0333	-0.3484	0.0604	0.3083	-0.3668	-0.0498	-0.2912	-0.0657	-0.4513	-0.1192	-0.2955	10.2741	36.5605	120.8149
5	5.6587	-0.6979	1.1394	5.4493	0.164	6.948	0.0396	-0.1873	0.5825	0.0746	0.0607	0.0153	-1.3215	0.0192	-0.1003	0.1037	-0.1801	0.2407	-0.5002	-0.0823	-0.3917	6.502	61.458	98.0193
6	6.0927	-0.418	-1.2453	5.6483	-0.0725	6.6649	0.2679	0.1283	-0.0329	0.1356	0.1678	-1.4429	-0.4997	1.2666	-0.4357	-0.451	-0.2267	0.014	0.0288	-0.3843	0.1385	31.6052	39.5986	94.8288
7	4.2907	-0.4151	-0.3756	4.3009	0.1259	6.3849	0.3735	0.4886	-0.3022	-1.05	-0.0358	0.3759	0.0569	-0.372	-0.3377	-0.0891	0.2871	-0.0612	-0.4282	0.1051	-0.286	-10.2563	36.5384	56.0593
8	5.4657	1.0617	1.5857	6.4976	0.0366	5.7847	0.0382	0.2547	0.5634	-0.0324	0.0924	-0.0265	-1.258	-0.0567	-0.1306	0.0905	0.1853	0.2544	-0.4619	0.085	-0.4012	-6.4823	61.4858	78.9239
9	5.9855	0.5863	-1.0027	5.5526	-0.3218	6.2124	0.2833	-0.1634	-0.0282	-0.0221	0.164	1.2655	-0.3757	-1.2043	-0.4473	-0.4304	0.2123	0.0012	0.0144	0.3935	0.11	-31.6034	39.5974	82.1222
10	4.5812	0.6613	0.0474	5.1139	0.7061	7.0794	0.3978	-0.5062	0.2456	1.0899	-0.053	0.337	-0.0158	-0.2541	-0.3448	-0.1176	-0.278	0.0621	-0.4198	0.1108	-0.3228	-10.2742	23.4216	120.8271
11	6.1766	-0.8585	-1.7828	6.0117	-0.2067	5.8667	0.0136	-0.2896	-0.6273	0.0657	0.1115	-0.0407	1.2587	-0.1246	-0.1251	0.0956	-0.1785	-0.2676	-0.5069	0.0764	-0.3862	-6.4836	-1.5026	98.0182
12	5.8932	-0.2936	0.8739	5.7566	-0.1183	5.5572	0.189	0.2103	0.1293	-0.0013	0.2297	1.4105	0.4442	-1.1663	-0.4188	-0.4344	-0.209	-0.0258	0.0697	0.3683	0.1132	-31.5983	20.3877	94.8338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-18 - -8
2	X-RAY DIFFRACTION	1	A	-1 - 15
3	X-RAY DIFFRACTION	1	A	23 - 158
4	X-RAY DIFFRACTION	2	B	1 - 158
5	X-RAY DIFFRACTION	3	C	1 - 158
6	X-RAY DIFFRACTION	4	D	-18 - -8
7	X-RAY DIFFRACTION	4	D	-1 - 15
8	X-RAY DIFFRACTION	4	D	23 - 158
9	X-RAY DIFFRACTION	5	E	1 - 158
10	X-RAY DIFFRACTION	6	F	1 - 158
11	X-RAY DIFFRACTION	7	G	-18 - -8
12	X-RAY DIFFRACTION	7	G	-1 - 15
13	X-RAY DIFFRACTION	7	G	23 - 158
14	X-RAY DIFFRACTION	8	H	1 - 158
15	X-RAY DIFFRACTION	9	I	1 - 158
16	X-RAY DIFFRACTION	10	J	-18 - -8
17	X-RAY DIFFRACTION	10	J	-1 - 15
18	X-RAY DIFFRACTION	10	J	23 - 158
19	X-RAY DIFFRACTION	11	K	1 - 158
20	X-RAY DIFFRACTION	12	L	1 - 158

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