SAXSdb — 5vjd

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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 2–359 Chain B； UniProt 2–359	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

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 5VJD	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 construct 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 construct 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
5GK5 Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution Deposited 2016-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Chain B 1–359（359 aa）	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
5GK5 Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution Deposited 2016-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–359（359 aa） Chain D 1–359（359 aa）	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
5GK5 Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution Deposited 2016-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–359（359 aa） Chain F 1–359（359 aa）	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
5GK5 Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution Deposited 2016-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–359（359 aa） Chain H 1–359（359 aa）	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
5GK6 Structure of E.Coli fructose 1,6-bisphosphate aldolase, Citrate bound form Deposited 2016-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（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 construct 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 construct 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
5VJE Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with D-glucitol 1,6-bisphosphate Deposited 2017-04-19	Different ligand/ion 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 13 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 1–358； UniProt 2–359 Author chain B； PDBConstruct 1–358； UniProt 2–359

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	5vjd
Deposition date deposition_date	2017-04-19
Structure title title	Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with DHAP
Keywords keywords	Glycolysis, 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	28.04 Å
Radius of gyration Rg (electron density) rg_electron	27.40 Å
Forward intensity I(0) i0	90549800.00
Molecular weight molecular_weight	75494.0 kDa
Excluded volume excluded_volume	94594 Å³
Envelope volume envelope_volume	109580 Å³
Hydration-shell volume shell_volume	33530 Å³
Envelope diameter envelope_diameter	101.9 Å
Shell Rg shell_rg	34.67 Å
Envelope Rg envelope_rg	27.64 Å
Shape Rg shape_rg	27.42 Å
Total Rg total_rg	28.04 Å
Total atoms total_atoms	10530
Residues n_residues	686
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	95.3 Å
Rg (real space) rg_real	28.14 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	9.0550e+07
I(0) uncertainty (real space) i0_real_error	1.3800e+06
Rg (reciprocal space) rg_reciprocal	28.11 Å
I(0) (reciprocal space) i0_reciprocal	90550000.0000
Solution quality estimate total_estimate	0.8645
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.461
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27340000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.973

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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	39060.0 kDa
EC 编号 ec_number	4.1.2.13
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	11558

SKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL

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

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 4 Entity 4 non-polymer

Description description	1,3-DIHYDROXYACETONEPHOSPHATE
Molecular weight formula_weight	170.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	971

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5vjda_
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	d5vjdb_
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 (2 domains)

Domain ID domain_id	5vjdA00
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	5vjdB00
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	57.174 Å
Unit-cell length b length_b	71.454 Å
Unit-cell length c length_c	88.185 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.701 Å
Low-resolution limit resolution_low	39.871 Å
R factor r_factor	0.1485
R_work r_work	0.1475
R_free r_free	0.1725

fit	/app/data/saxs_computation/vj/5vjd/5vjd.fit
pddf	/app/data/pr_computation/vj/5vjd/5vjd.pr.out
profile	/app/data/saxs_computation/vj/5vjd/5vjd.dat

Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with DHAP

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