PDB-1gu0: CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COE...

ID or keywords:

Entry

Database: PDB / ID: 1gu0

Title

CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR

Components

3-DEHYDROQUINATE DEHYDRATASE

Keywords

LYASE / TYPE II DEHYDROQUINASE / SHIKIMATE PATHWAY / DODECAMERIC QUATERNARY STRUCTURE / TETRAHEDRAL SYMMETRY

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

STREPTOMYCES COELICOLOR (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Roszak, A.W. / Krell, T. / Robinson, D. / Hunter, I.S. / Coggins, J.R. / Lapthorn, A.J.

Citation

Journal: Structure / Year: 2002
Title: The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor
Authors: Roszak, A.W. / Robinson, D. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.

History

Deposition	Jan 22, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 12, 2002	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 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_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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	1gu0.cif.gz	370.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1gu0.ent.gz	304.4 KB	Display	PDB format
PDBx/mmJSON format	1gu0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1gu0_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	1gu0_full_validation.pdf.gz	471.6 KB	Display
Data in XML	1gu0_validation.xml.gz	33.2 KB	Display
Data in CIF	1gu0_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/1gu0 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gu0	HTTPS FTP

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Related structure data

Related structure data	1d0iC 1gtzC 1gu1C 2dhqS 1gqn 1gqo 1guy 1gv1 1gvz 1qfe C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5yl5-d 1gtz-d 2bt4-d 5ypq-d 4zc1-d 1gu1-d 5b6p-d 5x47-d 6hsb-1 1gqo-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

hetero molecules

199 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)	116.200, 138.400, 141.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	H
8	1	I
9	1	J
10	1	K
11	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 2 - 150 / Label seq-ID: 2 - 150

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	H	H
8	I	I
9	J	J
10	K	K
11	L	L

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.00708, 0.92154, -0.38822), (-0.39202, -0.3546, -0.84887), (-0.91993, 0.1582, 0.35875)	8.23507, 85.55029, 40.90844
2	given	(0.00824, -0.39764, -0.9175), (0.91359, -0.37005, 0.16859), (0.40656, -0.83961, 0.36023)	71.29705, 17.09995, 61.55885
3	given	(-0.99996, 0.00502, -0.00776), (0.00909, 0.6851, -0.72839), (0.00166, -0.72843, -0.68512)	54.49592, 34.82314, 81.04834
4	given	(0.00352, 0.91859, -0.3952), (0.38144, 0.36409, 0.84967), (0.92439, -0.15373, -0.3491)	8.57029, -16.58185, 24.99649
5	given	(-0.01303, 0.39936, 0.9167), (-0.91922, -0.36559, 0.1462), (0.39352, -0.84075, 0.37186)	-16.52143, 67.34712, 39.30995
6	given	(-0.00983, -0.91991, 0.39201), (0.39635, -0.3635, -0.84307), (0.91805, 0.14709, 0.36818)	46.49717, 64.1228, -9.06398
7	given	(0.00707, -0.39838, -0.91719), (-0.91702, 0.36319, -0.16482), (0.39878, 0.84225, -0.36276)	71.15918, 52.28157, 5.18036
8	given	(-0.9999, -0.00746, -0.01185), (-0.00348, -0.68764, 0.72605), (-0.01356, 0.72602, 0.68754)	54.99685, 34.6108, -14.26512
9	given	(-0.01603, 0.39654, 0.91788), (0.91913, 0.36724, -0.14261), (-0.39363, 0.84136, -0.37035)	-16.17982, 1.6171, 27.03639
10	given	(0.99974, 0.00264, 0.02249), (0.00281, -0.99997, -0.00725), (0.02247, 0.00731, -0.99972)	-0.76468, 69.52921, 65.31114
11	given	(-0.00256, -0.92118, 0.38913), (0.41263, 0.35543, 0.83869), (0.91089, -0.15842, -0.38102)	46.60988, 5.75645, 76.06654

#1: Protein	3-DEHYDROQUINATE DEHYDRATASE / TYPE II 3-DEHYDROQUINATE HYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE Mass: 16569.605 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PDHQ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1740 / 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: 2.8 Å³/Da / Density % sol: 56.3 %
Crystal grow	pH: 8.5 Details: PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 1998
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87 Å / Relative weight: 1
Reflection	Resolution: 1.8→75 Å / Num. obs: 429534 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.057
Reflection shell	Resolution: 1.8→1.82 Å / % possible all: 93.5

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2DHQ

2dhq

Resolution: 2→24 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.937 / SU B: 7.428 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	12147	10 %	RANDOM
R_work	0.2	-	-	-
obs	0.204	6768	66.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Refinement step

Cycle: LAST / Resolution: 2→24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13327	0	32	1740	15099

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	13631
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12259
X-RAY DIFFRACTION	r_angle_refined_deg
X-RAY DIFFRACTION	r_angle_other_deg	2.056	1.925	18585
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	0.953	3	28290
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	2117
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	15736
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2736
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.3	3238
X-RAY DIFFRACTION	r_nbd_other	0.223	0.3	12353
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.265	0.5	1427
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.157	0.5	13
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.38	0.3	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.23	0.3	22
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.341	0.5	44
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	1.178	1.5	8848
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.921	2	14091
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.411	3	4783
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.549	4.5	4494
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

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.314	738
R_work	0.277	6768

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	0.1051	0.0234	0.0321	1.0431	-0.3617	0.6546	0.0169	-0.0043	0.0053	-0.0404	-0.0473	-0.1243	-0.188	0.0401	0.0304	0.1229	-0.0126	0.0401	0.2776	0.0568	0.3219	36.585	59.213	13.924
2	0.5475	0.3196	0.7359	1.5935	-0.1031	0.4548	0.0043	0.112	-0.0579	-0.2974	-0.0108	-0.226	0.0441	0.1326	0.0065	0.1265	0.008	0.0941	0.3195	0.0284	0.3064	35.336	31.172	1.659
3	0.3805	-0.2967	-0.0215	0.8437	0.0392	1.0427	0.004	-0.0135	0.0002	0.0062	-0.0924	-0.3024	-0.0351	0.3176	0.0884	0.0041	-0.0199	0.0321	0.4191	0.125	0.4894	57.566	38.194	21.788
4	0.5667	0.1273	-0.3872	0.2193	-0.4262	1.0251	0.0582	0.0475	0.1314	0.094	0.0219	0	-0.2593	-0.0274	-0.0802	0.1848	0.0334	0.0216	0.2592	0.0274	0.3173	18.026	65.494	28.343
5	0.0491	0.1171	0.2581	0.329	0.2698	0.1992	0.04	-0.0414	0.0345	0.1609	-0.0418	0.0098	-0.059	-0.0308	0.0018	0.2456	-0.0116	-0.0074	0.267	-0.0215	0.2857	18.78	55.011	57.194
6	0.526	0.1306	0.044	0.8535	-0.0045	0.5838	0.0427	-0.0426	0.0338	0.019	-0.0462	0.1752	-0.0958	-0.1191	0.0035	0.0716	0.033	0.019	0.2951	-0.0123	0.3314	-3.215	45.498	38.043
7	0.0644	-0.1598	-0.4638	0.6983	0.3169	1.0733	0.0399	0.0528	0.0133	-0.1143	-0.0517	0.03	0.0139	-0.0078	0.0118	0.0822	0.0158	0.008	0.2811	-0.0059	0.2705	19.257	14.277	8.703
8	0.4246	-0.4863	-0.2181	0.9799	-0.0533	0.8643	0.0023	0.0204	-0.0317	-0.0142	0.0097	0.1709	-0.0148	-0.1927	-0.012	0.0037	0.0104	-0.0019	0.3137	-0.0078	0.3255	-3.127	23.655	27.395
9	0.2259	-0.1421	-0.005	0.4906	-0.2886	0.8437	-0.0135	-0.0239	-0.0426	-0.0075	-0.0217	-0.0236	0.1077	-0.0159	0.0352	0.0458	-0.0176	0.0077	0.2575	0.0101	0.2697	17.947	3.673	37.462
10	0.5361	0.1384	-0.0768	0.6348	-0.3965	0.9525	-0.0592	-0.0584	0.071	0.0558	-0.0669	-0.3527	-0.069	0.3413	0.126	0.0552	-0.0285	-0.0588	0.4389	0.106	0.4959	57.266	31.033	45.059
11	0.0758	0.0268	-0.0081	0.8864	-0.2084	0.6823	-0.0557	0.0025	0.047	0.0721	-0.0133	-0.114	0.0475	0.085	0.069	0.081	0.0201	-0.0283	0.2856	0.055	0.2898	36.151	10.018	52.274
12	0.3924	-0.3804	-0.1953	1.8874	-0.1329	0.3744	-0.0462	-0.0734	0.1072	0.4087	0	-0.2046	-0.0653	0.1204	0.0462	0.2473	-0.0061	-0.0958	0.3023	-0.0006	0.3062	34.562	38.07	64.602

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 150
2	X-RAY DIFFRACTION	2	B	2 - 150
3	X-RAY DIFFRACTION	3	C	2 - 150
4	X-RAY DIFFRACTION	4	D	2 - 150
5	X-RAY DIFFRACTION	5	E	2 - 150
6	X-RAY DIFFRACTION	6	F	2 - 150
7	X-RAY DIFFRACTION	7	G	2 - 150
8	X-RAY DIFFRACTION	8	H	2 - 150
9	X-RAY DIFFRACTION	9	I	2 - 150
10	X-RAY DIFFRACTION	10	J	2 - 150
11	X-RAY DIFFRACTION	11	K	2 - 150
12	X-RAY DIFFRACTION	12	L	2 - 150

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