1q3g

MurA (Asp305Ala) liganded with tetrahedral reaction intermediate

Method: X-RAY DIFFRACTION Dmax: 221.1 Å Quality: GOOD

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

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

Enterobacter cloacae

UniProt P33038

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–419 Chain B; UniProt 1–419 Chain C; UniProt 1–419 Chain D; UniProt 1–419 Mutation:N67D,D305A Non-standard monomer:Yes (specific site not provided by mmCIF) UDA 3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;290 K;PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.65 Å R-free 0.253
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–419 Chain F; UniProt 1–419 Chain G; UniProt 1–419 Chain H; UniProt 1–419 Mutation:N67D,D305A Non-standard monomer:Yes (specific site not provided by mmCIF) UDA 3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;290 K;PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.65 Å R-free 0.253
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 1–419 Chain J; UniProt 1–419 Chain K; UniProt 1–419 Chain L; UniProt 1–419 Mutation:N67D,D305A Non-standard monomer:Yes (specific site not provided by mmCIF) UDA 3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;290 K;PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.65 Å R-free 0.253
4 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain W; UniProt 1–419 Chain X; UniProt 1–419 Chain Y; UniProt 1–419 Chain Z; UniProt 1–419 Mutation:N67D,D305A Non-standard monomer:Yes (specific site not provided by mmCIF) UDA 3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;290 K;PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.65 Å R-free 0.253

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.

24 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MURA_ENTCL
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–419; UniProt 1–419 Author chain B; PDBConstruct 1–419; UniProt 1–419 Author chain C; PDBConstruct 1–419; UniProt 1–419 Author chain D; PDBConstruct 1–419; UniProt 1–419 Author chain E; PDBConstruct 1–419; UniProt 1–419 Author chain F; PDBConstruct 1–419; UniProt 1–419 Author chain G; PDBConstruct 1–419; UniProt 1–419 Author chain H; PDBConstruct 1–419; UniProt 1–419 Author chain I; PDBConstruct 1–419; UniProt 1–419 Author chain J; PDBConstruct 1–419; UniProt 1–419 Author chain K; PDBConstruct 1–419; UniProt 1–419 Author chain L; PDBConstruct 1–419; UniProt 1–419 Author chain W; PDBConstruct 1–419; UniProt 1–419 Author chain X; PDBConstruct 1–419; UniProt 1–419 Author chain Y; PDBConstruct 1–419; UniProt 1–419 Author chain Z; PDBConstruct 1–419; UniProt 1–419

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 1q3g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q3g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1q3g
Deposition date deposition_date2003-07-29
Structure title titleMurA (Asp305Ala) liganded with tetrahedral reaction intermediate
Keywords keywordsinside-out alpha-beta barrel, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier64.39
Radius of gyration Rg (electron density) rg_electron64.22
Forward intensity I(0) i07507730000.00
Molecular weight molecular_weight729060.0 kDa
Excluded volume excluded_volume912440 ų
Envelope volume envelope_volume1215100 ų
Hydration-shell volume shell_volume154390 ų
Envelope diameter envelope_diameter222.0
Shell Rg shell_rg68.20
Envelope Rg envelope_rg62.52
Shape Rg shape_rg64.23
Total Rg total_rg64.22
Total atoms total_atoms51088
Residues n_residues6688
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax221.1
Rg (real space) rg_real64.35
Rg uncertainty (real space) rg_real_error2.08
I(0) (real space) i0_real7.5080e+09
I(0) uncertainty (real space) i0_real_error1.6410e+08
Rg (reciprocal space) rg_reciprocal64.40
I(0) (reciprocal space) i0_reciprocal7508000000.0000
Solution quality estimate total_estimate0.8564
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary82.9
Skewness Skewness skewness0.322
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha1880000000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.644

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1q3ga_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3ge_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gk_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gl_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gw_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gx_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gy_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT
Domain ID domain_idd1q3gz_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.2 — EPT/RTPC-like
Family Family familyd.68.2.2 — Enolpyruvate transferase, EPT

CATH v4.4 (32 domains)

Domain ID domain_id1q3gA01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gA02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gB01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gB02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gC01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gC02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gD01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gD02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gE01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gE02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gF01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gF02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gG01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gG02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gH01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gH02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gI01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gI02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gJ01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gJ02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gK01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gK02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gL01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gL02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gW01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gW02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gX01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gX02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gY01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gY02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gZ01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain
Domain ID domain_id1q3gZ02
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily10 — Enolpyruvate transferase domain

8. Citations (1)

9. Files and Curves (10)