SAXSdb — 1cd5

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

PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE)

Escherichia coli

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–266	Not recorded	No other associated polymer	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

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 1CD5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 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 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 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 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 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 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 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 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
2WU1 Glucosamine-6-Phosphate Deaminase Complexed with the Allosteric Activator N-Acetyl-Glucoamine-6-Phosphate both in the Active and Allosteric sites. Deposited 2009-09-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–266（266 aa）	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
2WU1 Glucosamine-6-Phosphate Deaminase Complexed with the Allosteric Activator N-Acetyl-Glucoamine-6-Phosphate both in the Active and Allosteric sites. Deposited 2009-09-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–266（266 aa）	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

9 other PDB entries and 13 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cd5
Deposition date deposition_date	1999-03-05
Structure title title	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER
Keywords keywords	ALLOSTERIC ENZYME, ENTROPIC EFFECTS, ALDOSE-KETOSE ISOMERASE, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.28 Å
Radius of gyration Rg (electron density) rg_electron	18.03 Å
Forward intensity I(0) i0	15586300.00
Molecular weight molecular_weight	29771.0 kDa
Excluded volume excluded_volume	37289 Å³
Envelope volume envelope_volume	42371 Å³
Hydration-shell volume shell_volume	19441 Å³
Envelope diameter envelope_diameter	59.3 Å
Shell Rg shell_rg	24.52 Å
Envelope Rg envelope_rg	18.20 Å
Shape Rg shape_rg	18.03 Å
Total Rg total_rg	18.98 Å
Total atoms total_atoms	2558
Residues n_residues	266
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

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

Maximum dimension Dmax dmax	58.9 Å
Rg (real space) rg_real	19.13 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.5590e+07
I(0) uncertainty (real space) i0_real_error	1.8070e+05
Rg (reciprocal space) rg_reciprocal	19.15 Å
I(0) (reciprocal space) i0_reciprocal	15590000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.078
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2952000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cd5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.1 — NagB-like

CATH v4.4 (1 domains)

Domain ID domain_id	1cd5A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1360 —

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8. Citations (1)

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Unit-cell length a length_a	129.810 Å
Unit-cell length b length_b	129.810 Å
Unit-cell length c length_c	139.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2070
R_free r_free	0.2520

Description description	PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE)
Molecular weight formula_weight	29812.2 kDa
EC 编号 ec_number	5.3.1.10
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2981

GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER

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

PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

fit	/app/data/saxs_computation/cd/1cd5/1cd5.fit
pddf	/app/data/pr_computation/cd/1cd5/1cd5.pr.out
profile	/app/data/saxs_computation/cd/1cd5/1cd5.dat