1gu1

Crystal structure of type II dehydroquinase from Streptomyces coelicolor complexed with 2,3-anhydro-quinic acid

Method: X-RAY DIFFRACTION D_max: 105.6 Å Quality: REASONABLE

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

3-DEHYDROQUINATE DEHYDRATASE

STREPTOMYCES COELICOLOR

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–156 Chain B； UniProt 1–156 Chain C； UniProt 1–156 Chain D； UniProt 1–156 Chain E； UniProt 1–156 Chain F； UniProt 1–156 Chain G； UniProt 1–156 Chain H； UniProt 1–156 Chain I； UniProt 1–156 Chain J； UniProt 1–156 Chain K； UniProt 1–156 Chain L； UniProt 1–156	Not recorded	FA1 2,3 -ANHYDRO-QUINIC ACID × 12 GOL GLYCEROL × 12 TLA L(+)-TARTARIC ACID × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50	Resolution 1.80 Å R-free 0.200

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1GU1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0I CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS Deposited 1999-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 2–157（156 aa） Chain B 2–157（156 aa） Chain C 2–157（156 aa） Chain D 2–157（156 aa） Chain E 2–157（156 aa） Chain F 2–157（156 aa） Chain G 2–157（156 aa） Chain H 2–157（156 aa） Chain I 2–157（156 aa） Chain J 2–157（156 aa） Chain K 2–157（156 aa） Chain L 2–157（156 aa）	Not recorded	PO4 PHOSPHATE ION × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.223
1GTZ Structure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A MUTANT IN COMPLEX WITH DEHYDROSHIKIMATE Deposited 2002-01-22	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–156（156 aa） Chain B 1–156（156 aa） Chain C 1–156（156 aa） Chain D 1–156（156 aa） Chain E 1–156（156 aa） Chain F 1–156（156 aa） Chain G 1–156（156 aa） Chain H 1–156（156 aa） Chain I 1–156（156 aa） Chain J 1–156（156 aa） Chain K 1–156（156 aa） Chain L 1–156（156 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 DHK 3-DEHYDROSHIKIMATE × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50	Resolution 1.60 Å R-free 0.221
1GU0 CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR Deposited 2002-01-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–156（156 aa） Chain B 1–156（156 aa） Chain C 1–156（156 aa） Chain D 1–156（156 aa） Chain E 1–156（156 aa） Chain F 1–156（156 aa） Chain G 1–156（156 aa） Chain H 1–156（156 aa） Chain I 1–156（156 aa） Chain J 1–156（156 aa） Chain K 1–156（156 aa） Chain L 1–156（156 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50	Resolution 2.00 Å R-free 0.242
1V1J Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro Deposited 2004-04-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–156（156 aa） Chain B 1–156（156 aa） Chain C 1–156（156 aa） Chain D 1–156（156 aa） Chain E 1–156（156 aa） Chain F 1–156（156 aa） Chain G 1–156（156 aa） Chain H 1–156（156 aa） Chain I 1–156（156 aa） Chain J 1–156（156 aa） Chain K 1–156（156 aa） Chain L 1–156（156 aa）	Not recorded	FA3 2-ANHYDRO-3-FLUORO-QUINIC ACID × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PEG 8000, NA/K PHOSPHATE, TRIS BUFFER, pH 7.50	Resolution 2.20 Å R-free 0.238
2BT4 Type II Dehydroquinase inhibitor complex Deposited 2005-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–157（157 aa） Chain B 1–157（157 aa） Chain C 1–157（157 aa） Chain D 1–157（157 aa） Chain E 1–157（157 aa） Chain F 1–157（157 aa） Chain G 1–157（157 aa） Chain H 1–157（157 aa） Chain I 1–157（157 aa） Chain J 1–157（157 aa） Chain K 1–157（157 aa） Chain L 1–157（157 aa）	Not recorded	CA2 (1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID × 12 PO4 PHOSPHATE ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；15% PEG8K, 0.2M NAKPHOSPHATE, 0.1M MOPS/HCL PH6.5, pH 6.50	Resolution 1.70 Å R-free 0.248
2CJF TYPE II DEHYDROQUINASE INHIBITOR COMPLEX Deposited 2006-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–157（157 aa） Chain B 1–157（157 aa） Chain C 1–157（157 aa） Chain D 1–157（157 aa） Chain E 1–157（157 aa） Chain F 1–157（157 aa） Chain G 1–157（157 aa） Chain H 1–157（157 aa） Chain I 1–157（157 aa） Chain J 1–157（157 aa） Chain K 1–157（157 aa） Chain L 1–157（157 aa）	Not recorded	RP4 (1S,4S,5S)-1,4,5-TRIHYDROXY-3-[3-(PHENYLTHIO)PHENYL]CYCLOHEX-2-ENE-1-CARBOXYLIC ACID × 12 GOL GLYCEROL × 12 PO4 PHOSPHATE ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；PROTEIN AT 6MG/ML WAS EQUILIBRATED AGAINST A SOLUTION 15% PEG 8K, 0.1M HEPES BUFFER PH 7.5 USING THE SITING DROP METHOD.	Resolution 1.95 Å R-free 0.334

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AROQ_STRCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 1–156 Author chain B； PDBConstruct 1–156； UniProt 1–156 Author chain C； PDBConstruct 1–156； UniProt 1–156 Author chain D； PDBConstruct 1–156； UniProt 1–156 Author chain E； PDBConstruct 1–156； UniProt 1–156 Author chain F； PDBConstruct 1–156； UniProt 1–156 Author chain G； PDBConstruct 1–156； UniProt 1–156 Author chain H； PDBConstruct 1–156； UniProt 1–156 Author chain I； PDBConstruct 1–156； UniProt 1–156 Author chain J； PDBConstruct 1–156； UniProt 1–156 Author chain K； PDBConstruct 1–156； UniProt 1–156 Author chain L； PDBConstruct 1–156； UniProt 1–156

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gu1
Deposition date deposition_date	2002-01-22
Structure title title	Crystal structure of type II dehydroquinase from Streptomyces coelicolor complexed with 2,3-anhydro-quinic acid
Keywords keywords	LYASE, SHIKIMATE PATHWAY, TETRAHEDRAL SYMMETRY; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.07 Å
Radius of gyration Rg (electron density) rg_electron	35.19 Å
Forward intensity I(0) i0	637293000.00
Molecular weight molecular_weight	196490.0 kDa
Excluded volume excluded_volume	242220 Å³
Envelope volume envelope_volume	293240 Å³
Hydration-shell volume shell_volume	65282 Å³
Envelope diameter envelope_diameter	106.4 Å
Shell Rg shell_rg	44.70 Å
Envelope Rg envelope_rg	34.50 Å
Shape Rg shape_rg	35.14 Å
Total Rg total_rg	35.88 Å
Total atoms total_atoms	13820
Residues n_residues	1788
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	105.6 Å
Rg (real space) rg_real	35.73 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	6.3730e+08
I(0) uncertainty (real space) i0_real_error	8.7530e+06
Rg (reciprocal space) rg_reciprocal	35.94 Å
I(0) (reciprocal space) i0_reciprocal	637400000.0000
Solution quality estimate total_estimate	0.6852
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.4 Å
Skewness Skewness skewness	-0.068
Kurtosis Kurtosis kurtosis	-0.555
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	283800000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.955; Smooth: 0.923

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	3-DEHYDROQUINATE DEHYDRATASE
Molecular weight formula_weight	16569.6 kDa
EC 编号 ec_number	4.2.1.10
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	16578

PRSLANAPIMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHEARLNHCGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAGCGVQGYVFGVERIAALAGAGSARA

来源 Source

来源生物 organism	STREPTOMYCES COELICOLOR
NCBI Class编号 ncbi_taxonomy_id	1902
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2,3 -ANHYDRO-QUINIC ACID
Molecular weight formula_weight	174.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2634

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1gu1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d1gu1l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

CATH v4.4 (12 domains)

Domain ID domain_id	1gu1A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1J00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1K00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	1gu1L00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

▶

8. Citations (1)

▶

Unit-cell length a length_a	113.600 Å
Unit-cell length b length_b	138.400 Å
Unit-cell length c length_c	141.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	22.000 Å
R factor r_factor	—
R_work r_work	0.1550
R_free r_free	0.2000

fit	/app/data/saxs_computation/gu/1gu1/1gu1.fit
pddf	/app/data/pr_computation/gu/1gu1/1gu1.pr.out
profile	/app/data/saxs_computation/gu/1gu1/1gu1.dat