SAXSdb — 1frz

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

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 Chain B； UniProt 1–266	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

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 1FRZ	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 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）	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 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 construct 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）	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 construct Different mutation/modification 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 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
1FS5 A DISCOVERY OF THREE ALTERNATE CONFORMATIONS IN THE ACTIVE SITE OF GLUCOSAMINE-6-PHOSPHATE ISOMERASE Deposited 2000-09-08	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 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）	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 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）	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 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 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）	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 construct 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
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 construct Different mutation/modification 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 construct Different mutation/modification 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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1frz
Deposition date deposition_date	2000-09-07
Structure title title	GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION
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	31.92 Å
Radius of gyration Rg (electron density) rg_electron	31.70 Å
Forward intensity I(0) i0	58317500.00
Molecular weight molecular_weight	60145.0 kDa
Excluded volume excluded_volume	75187 Å³
Envelope volume envelope_volume	94112 Å³
Hydration-shell volume shell_volume	26167 Å³
Envelope diameter envelope_diameter	103.9 Å
Shell Rg shell_rg	36.49 Å
Envelope Rg envelope_rg	31.50 Å
Shape Rg shape_rg	31.78 Å
Total Rg total_rg	31.83 Å
Total atoms total_atoms	4222
Residues n_residues	532
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	104.5 Å
Rg (real space) rg_real	32.25 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	5.8320e+07
I(0) uncertainty (real space) i0_real_error	8.5820e+05
Rg (reciprocal space) rg_reciprocal	32.12 Å
I(0) (reciprocal space) i0_reciprocal	58310000.0000
Solution quality estimate total_estimate	0.7939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.800
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17820000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.567; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.679; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4457

MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
Molecular weight formula_weight	301.2 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1frza_
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

Domain ID domain_id	d1frzb_
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 (2 domains)

Domain ID domain_id	1frzA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1360 —

Domain ID domain_id	1frzB00
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 (3)

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Unit-cell length a length_a	125.720 Å
Unit-cell length b length_b	125.720 Å
Unit-cell length c length_c	223.950 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1990
R_free r_free	0.2270

fit	/app/data/saxs_computation/fr/1frz/1frz.fit
pddf	/app/data/pr_computation/fr/1frz/1frz.pr.out
profile	/app/data/saxs_computation/fr/1frz/1frz.dat

GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION

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

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