SAXSdb — 5gk5

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

Fructose-bisphosphate aldolase class 2

Escherichia coli (strain K12)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–359 Chain B； UniProt 1–359	Not recorded	GOL GLYCEROL × 2 ZN ZINC ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 1.90 Å R-free 0.207
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–359 Chain D； UniProt 1–359	Not recorded	GOL GLYCEROL × 2 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 1.90 Å R-free 0.207
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–359 Chain F； UniProt 1–359	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 1.90 Å R-free 0.207
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–359 Chain H； UniProt 1–359	Not recorded	GOL GLYCEROL × 2 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 1.90 Å R-free 0.207

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 5GK5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B57 CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE IN COMPLEX WITH PHOSPHOGLYCOLOHYDROXAMATE Deposited 1999-01-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–358（358 aa） Chain B 1–358（358 aa）	Not recorded	ZN ZINC ION × 7 NA SODIUM ION × 2 CL CHLORIDE ION × 1 PGH PHOSPHOGLYCOLOHYDROXAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.230
1DOS STRUCTURE OF FRUCTOSE-BISPHOSPHATE ALDOLASE Deposited 1996-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–358（358 aa） Chain B 1–358（358 aa）	Not recorded	ZN ZINC ION × 2 NH4 AMMONIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.67 Å R-free 0.204
1ZEN CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE Deposited 1996-07-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–358（358 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.326
5GK3 Native structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.8 Angstrom resolution Deposited 2016-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	Not recorded	GOL GLYCEROL × 3 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 5% fructose 1,6-bisphosphatase, 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 1.80 Å R-free 0.189
5GK4 Native structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 2.0 Angstrom resolution Deposited 2016-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	Not recorded	GOL GLYCEROL × 2 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 5% fructose 1,6-bisphosphatase, 0.1M Tris pH 7.0, and 15% PEG 4000	Resolution 2.00 Å R-free 0.200
5GK6 Structure of E.Coli fructose 1,6-bisphosphate aldolase, Citrate bound form Deposited 2016-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	Not recorded	ZN ZINC ION × 2 CIT CITRIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2M ammonium acetate, 5mM aldose, 0.1M citrate buffer pH 7.0, and 15% PEG 4000	Resolution 1.80 Å R-free 0.194
5GK7 Structure of E.Coli fructose 1,6-bisphosphate aldolase bound to Tris Deposited 2016-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	Not recorded	GOL GLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2 M ammonium acetate, 5mM fructose 1,6-bisphosphatase, 0.1 M Tris/HCl pH 7.0, and 15% PEG 4000	Resolution 1.80 Å R-free 0.197
5GK8 Structure of E.Coli fructose 1,6-bisphosphate aldolase, Acetate bound form Deposited 2016-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	Not recorded	GOL GLYCEROL × 4 ACT ACETATE ION × 2 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.2 M ammonium acetate, 5% fructose 1,6-bisphosphatase, 0.1 M Tris pH 7.0, and 15% PEG 4000	Resolution 2.00 Å R-free 0.200
5VJD Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with DHAP Deposited 2017-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–359（358 aa） Chain B 2–359（358 aa）	Not recorded	NA SODIUM ION × 4 ZN ZINC ION × 2 13P 1,3-DIHYDROXYACETONEPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, MgCl2, Hepes buffer	Resolution 1.70 Å R-free 0.172
5VJE Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with D-glucitol 1,6-bisphosphate Deposited 2017-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–359（358 aa） Chain B 2–359（358 aa）	Not recorded	NA SODIUM ION × 4 GOS D-Glucitol-1,6-bisphosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, MgCl2, Hepes buffer	Resolution 1.65 Å R-free 0.164

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ALF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–359； UniProt 1–359 Author chain B； PDBConstruct 1–359； UniProt 1–359 Author chain C； PDBConstruct 1–359； UniProt 1–359 Author chain D； PDBConstruct 1–359； UniProt 1–359 Author chain E； PDBConstruct 1–359； UniProt 1–359 Author chain F； PDBConstruct 1–359； UniProt 1–359 Author chain G； PDBConstruct 1–359； UniProt 1–359 Author chain H； PDBConstruct 1–359； UniProt 1–359

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	5gk5
Deposition date deposition_date	2016-07-03
Structure title title	Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution
Keywords keywords	FBA apo3, LYASE; LYASE
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	49.77 Å
Radius of gyration Rg (electron density) rg_electron	49.19 Å
Forward intensity I(0) i0	1227590000.00
Molecular weight molecular_weight	293590.0 kDa
Excluded volume excluded_volume	367740 Å³
Envelope volume envelope_volume	500010 Å³
Hydration-shell volume shell_volume	84201 Å³
Envelope diameter envelope_diameter	153.8 Å
Shell Rg shell_rg	54.09 Å
Envelope Rg envelope_rg	47.72 Å
Shape Rg shape_rg	49.20 Å
Total Rg total_rg	49.33 Å
Total atoms total_atoms	20650
Residues n_residues	2661
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	154.3 Å
Rg (real space) rg_real	49.39 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	1.2280e+09
I(0) uncertainty (real space) i0_real_error	1.9090e+07
Rg (reciprocal space) rg_reciprocal	49.76 Å
I(0) (reciprocal space) i0_reciprocal	1228000000.0000
Solution quality estimate total_estimate	0.8302
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.5 Å
Skewness Skewness skewness	-0.018
Kurtosis Kurtosis kurtosis	-0.691
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63920000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fructose-bisphosphate aldolase class 2
Molecular weight formula_weight	39191.2 kDa
EC 编号 ec_number	4.1.2.13
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	21789

MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1139

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5gk5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

Domain ID domain_id	d5gk5h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.2 — Class II FBP aldolase

CATH v4.4 (8 domains)

Domain ID domain_id	5gk5A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5E00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5F00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5G00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5gk5H00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	72.834 Å
Unit-cell length b length_b	90.535 Å
Unit-cell length c length_c	113.733 Å
Unit-cell angle α angle_alpha	90.07 °
Unit-cell angle β angle_beta	90.01 °
Unit-cell angle γ angle_gamma	90.21 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	22.055 Å
R factor r_factor	0.1740
R_work r_work	0.1723
R_free r_free	0.2068

fit	/app/data/saxs_computation/gk/5gk5/5gk5.fit
pddf	/app/data/pr_computation/gk/5gk5/5gk5.pr.out
profile	/app/data/saxs_computation/gk/5gk5/5gk5.dat

Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution

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

Fructose-bisphosphate aldolase class 2

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