1gtz

Structure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A MUTANT IN COMPLEX WITH DEHYDROSHIKIMATE

Method: X-RAY DIFFRACTION D_max: 105.0 Å Quality: GOOD

▼

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	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

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 1GTZ	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 mutation/modification 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
1GU0 CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR 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）	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
1GU1 Crystal structure of type II dehydroquinase from Streptomyces coelicolor complexed with 2,3-anhydro-quinic acid 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）	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
1V1J Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro Deposited 2004-04-16	Different mutation/modification 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 mutation/modification 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 mutation/modification 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	1gtz
Deposition date deposition_date	2002-01-22
Structure title title	Structure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A MUTANT IN COMPLEX WITH DEHYDROSHIKIMATE
Keywords keywords	;LYASE, TYPE II DEHYDROQUINASE, SHIKIMATE PATHWAY, DODECAMERIC QUATERNARY STRUCTURE, TETRAHEDRAL SYMMETRY AROMATIC AMINO ACID BIOSYNTHESIS ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	36.23 Å
Radius of gyration Rg (electron density) rg_electron	35.28 Å
Forward intensity I(0) i0	605638000.00
Molecular weight molecular_weight	192550.0 kDa
Excluded volume excluded_volume	237830 Å³
Envelope volume envelope_volume	295120 Å³
Hydration-shell volume shell_volume	65590 Å³
Envelope diameter envelope_diameter	106.5 Å
Shell Rg shell_rg	44.82 Å
Envelope Rg envelope_rg	34.56 Å
Shape Rg shape_rg	35.23 Å
Total Rg total_rg	36.01 Å
Total atoms total_atoms	13556
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	105.0 Å
Rg (real space) rg_real	35.89 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	6.0560e+08
I(0) uncertainty (real space) i0_real_error	9.0820e+06
Rg (reciprocal space) rg_reciprocal	36.10 Å
I(0) (reciprocal space) i0_reciprocal	605800000.0000
Solution quality estimate total_estimate	0.8937
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.5 Å
Skewness Skewness skewness	-0.068
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	318200000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.895

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	3-DEHYDROQUINATE DEHYDRATASE
Molecular weight formula_weight	16483.5 kDa
EC 编号 ec_number	4.2.1.10
Mutation mutation	YES
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	15328

PRSLANAPIMILNGPNLNLLGQAQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHEARLNHCGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAGCGVQGYVFGVERIAALAGAGSARA

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-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 3 Entity 3 non-polymer

Description description	3-DEHYDROSHIKIMATE
Molecular weight formula_weight	174.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1580

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1gtza_
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	d1gtzb_
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	d1gtzc_
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	d1gtzd_
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	d1gtze_
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	d1gtzf_
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	d1gtzg_
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	d1gtzh_
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	d1gtzi_
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	d1gtzj_
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	d1gtzk_
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	d1gtzl_
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	1gtzA00
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	1gtzB00
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	1gtzC00
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	1gtzD00
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	1gtzE00
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	1gtzF00
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	1gtzG00
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	1gtzH00
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	1gtzI00
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	1gtzJ00
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	1gtzK00
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	1gtzL00
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	86.100 Å
Unit-cell length b length_b	136.200 Å
Unit-cell length c length_c	96.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	—
R_work r_work	0.1790
R_free r_free	0.2210

fit	/app/data/saxs_computation/gt/1gtz/1gtz.fit
pddf	/app/data/pr_computation/gt/1gtz/1gtz.pr.out
profile	/app/data/saxs_computation/gt/1gtz/1gtz.dat