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2wu1

Glucosamine-6-Phosphate Deaminase Complexed with the Allosteric Activator N-Acetyl-Glucoamine-6-Phosphate both in the Active and Allosteric sites.

Method: X-RAY DIFFRACTION Dmax: 104.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GLUCOSAMINE-6-PHOSPHATE DEAMINASE

ESCHERICHIA COLI

UniProt P0A759

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–266 Not recorded 16G 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 FGS 5-(ACETYLAMINO)-5-DEOXY-1-O-PHOSPHONO-L-IDITOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；SODIUM ACETATE, HEPES, N-ACETYL-GLUCOSAMINE-6-PHOSPHATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP AT 291K Resolution 2.20 Å R-free 0.191
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–266 Not recorded 16G 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 FGS 5-(ACETYLAMINO)-5-DEOXY-1-O-PHOSPHONO-L-IDITOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；SODIUM ACETATE, HEPES, N-ACETYL-GLUCOSAMINE-6-PHOSPHATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP AT 291K Resolution 2.20 Å R-free 0.191

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 2WU1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CD5 GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER Deposited 1999-03-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；sodium acetate, hepes, pH 7.0, VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.252
1DEA STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION Deposited 1995-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Chain B 1–266（266 aa）
Not recorded PO4 PHOSPHATE ION × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1DEA STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION Deposited 1995-09-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–266（266 aa）
Not recorded PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1DEA STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION Deposited 1995-09-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–266（266 aa）
Not recorded PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1FQO GLUCOSAMINE 6-PHOSPHATE DEAMINASE COMPLEXED WITH THE SUBSTRATE OF THE REVERSE REACTION FRUCTOSE 6-PHOSPHATE (OPEN FORM) Deposited 2000-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Chain B 1–266（266 aa）
Not recorded F6R FRUCTOSE -6-PHOSPHATE × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；sodium acetate, HEPES, fructose 6-phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K
Resolution 2.20 Å R-free 0.233
1FRZ GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION Deposited 2000-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Chain B 1–266（266 aa）
Not recorded 16G 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K
Resolution 2.20 Å R-free 0.227
1FS5 A DISCOVERY OF THREE ALTERNATE CONFORMATIONS IN THE ACTIVE SITE OF GLUCOSAMINE-6-PHOSPHATE ISOMERASE Deposited 2000-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Chain B 1–266（266 aa）
Not recorded 16G 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 6 TLA L(+)-TARTARIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；HEPES, sodium potassium tatrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K
Resolution 1.73 Å R-free 0.251
1FS6 GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER, AT 2.2A RESOLUTION Deposited 2000-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；HEPES, sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 291K
Resolution 2.20 Å R-free 0.235
1FSF GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER, AT 1.9A RESOLUTION Deposited 2000-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；HEPES, sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 291K
Resolution 1.90 Å R-free 0.232
1HOR STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION Deposited 1995-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Chain B 1–266（266 aa）
Not recorded PO4 PHOSPHATE ION × 6 AGP 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1JT9 Structure of the mutant F174A T form of the Glucosamine-6-Phosphate deaminase from E.coli Deposited 2001-08-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–266（266 aa）
Mutation：F174A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；HEPES, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.06 Å R-free 0.224
1JT9 Structure of the mutant F174A T form of the Glucosamine-6-Phosphate deaminase from E.coli Deposited 2001-08-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–266（266 aa）
Mutation：F174A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；HEPES, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.06 Å R-free 0.224

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NAGB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–266； UniProt 1–266 Author chain B； PDBConstruct 1–266； UniProt 1–266

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 2wu1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2wu1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2wu1
Deposition date deposition_date2009-09-25
Structure title titleGlucosamine-6-Phosphate Deaminase Complexed with the Allosteric Activator N-Acetyl-Glucoamine-6-Phosphate both in the Active and Allosteric sites.
Keywords keywordsALLOSTERIC ENZYME, CARBOHYDRATE METABOLISM, ALDOSE-KETOSE ISOMERASE, HYDROLASE, DISULFIDE BOND, ENTROPIC EFFECTS; HYDROLASE
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_guinier31.83 Å
Radius of gyration Rg (electron density) rg_electron31.65 Å
Forward intensity I(0) i059985100.00
Molecular weight molecular_weight60751.0 kDa
Excluded volume excluded_volume75815 ų
Envelope volume envelope_volume93900 ų
Hydration-shell volume shell_volume26126 ų
Envelope diameter envelope_diameter103.5 Å
Shell Rg shell_rg36.43 Å
Envelope Rg envelope_rg31.47 Å
Shape Rg shape_rg31.74 Å
Total Rg total_rg31.76 Å
Total atoms total_atoms4260
Residues n_residues532
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 dmax104.2 Å
Rg (real space) rg_real32.16 Å
Rg uncertainty (real space) rg_real_error0.98 Å
I(0) (real space) i0_real5.9990e+07
I(0) uncertainty (real space) i0_real_error1.1190e+06
Rg (reciprocal space) rg_reciprocal32.03 Å
I(0) (reciprocal space) i0_reciprocal59980000.0000
Solution quality estimate total_estimate0.7923
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.0 Å
Skewness Skewness skewness0.420
Kurtosis Kurtosis kurtosis-0.801
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19860000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.564; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.671; Smooth: 0.932
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2wu1a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamilyc.124.1 — NagB/RpiA/CoA transferase-like
Family Family familyc.124.1.1 — NagB-like
Domain ID domain_idd2wu1b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamilyc.124.1 — NagB/RpiA/CoA transferase-like
Family Family familyc.124.1.1 — NagB-like

CATH v4.4 (2 domains)

Domain ID domain_id2wu1A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1360 —
Domain ID domain_id2wu1B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1360 —
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8. Citations (1)

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9. Files and Curves (10)