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1v1j

Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro

Method: X-RAY DIFFRACTION Dmax: 105.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-DEHYDROQUINATE DEHYDRATASE

STREPTOMYCES COELICOLOR

UniProt P15474

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 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

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 1V1J 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 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）
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 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 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 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 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
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 2–157； UniProt 1–156 Author chain B； PDBConstruct 2–157； UniProt 1–156 Author chain C； PDBConstruct 2–157； UniProt 1–156 Author chain D； PDBConstruct 2–157； UniProt 1–156 Author chain E； PDBConstruct 2–157； UniProt 1–156 Author chain F； PDBConstruct 2–157； UniProt 1–156 Author chain G； PDBConstruct 2–157； UniProt 1–156 Author chain H； PDBConstruct 2–157； UniProt 1–156 Author chain I； PDBConstruct 2–157； UniProt 1–156 Author chain J； PDBConstruct 2–157； UniProt 1–156 Author chain K； PDBConstruct 2–157； UniProt 1–156 Author chain L； PDBConstruct 2–157； 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

SAXS profile for 1v1j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1v1j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1v1j
Deposition date deposition_date2004-04-16
Structure title titleCrystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro
Keywords keywordsDHQ, SHIKIMATE, DEHYDROQUINASE, AROMATIC AMINO ACID BIOSYNTHESIS, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.26 Å
Radius of gyration Rg (electron density) rg_electron35.36 Å
Forward intensity I(0) i0615738000.00
Molecular weight molecular_weight194270.0 kDa
Excluded volume excluded_volume239910 ų
Envelope volume envelope_volume295470 ų
Hydration-shell volume shell_volume65351 ų
Envelope diameter envelope_diameter105.6 Å
Shell Rg shell_rg45.06 Å
Envelope Rg envelope_rg34.69 Å
Shape Rg shape_rg35.32 Å
Total Rg total_rg36.07 Å
Total atoms total_atoms13676
Residues n_residues1800
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.1 Å
Rg (real space) rg_real35.92 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real6.1570e+08
I(0) uncertainty (real space) i0_real_error1.0310e+07
Rg (reciprocal space) rg_reciprocal36.13 Å
I(0) (reciprocal space) i0_reciprocal615900000.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.5 Å
Skewness Skewness skewness-0.075
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha271300000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.893
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1v1ja_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1je_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1ji_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jj_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jk_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase
Domain ID domain_idd1v1jl_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.13 — Type II 3-dehydroquinate dehydratase
Family Family familyc.23.13.1 — Type II 3-dehydroquinate dehydratase

CATH v4.4 (12 domains)

Domain ID domain_id1v1jA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jI00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jJ00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jK00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
Domain ID domain_id1v1jL00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily9100 — Dehydroquinase, class II
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8. Citations (1)

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9. Files and Curves (10)