SAXSdb — 2eph

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

Fructose-bisphosphate aldolase

Plasmodium falciparum

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–369 Chain B； UniProt 1–369 Chain C； UniProt 1–369 Chain D； UniProt 1–369	Not recorded	PbTRAP × 1 （P90573）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5 mM TRAP-tail, 0.5% n-dodecyl-beta-D-maltoside, 50 mM cacodylic acid pH 6.0, 20% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.250

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 2EPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5C FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM PLASMODIUM FALCIPARUM Deposited 1998-02-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–369（368 aa） Chain B 2–369（368 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.6；VAPOR DIFFUSION: 2.0 M AMMONIUM SULFATE/5% 2-PROPANOL, pH 7.6, vapor diffusion	Resolution 3.00 Å R-free 0.329
2PC4 Crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP-tail determined at 2.4 angstrom resolution Deposited 2007-03-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–369（369 aa） Chain B 1–369（369 aa） Chain C 1–369（369 aa） Chain D 1–369（369 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5 mM TRAP-tail, 0.5% n-dodecyl-beta-D-maltoside, 50 mM Cacodylic acid pH 6.0, 20% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.250

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ALF_PLAFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–369； UniProt 1–369 Author chain B； PDBConstruct 1–369； UniProt 1–369 Author chain C； PDBConstruct 1–369； UniProt 1–369 Author chain D； PDBConstruct 1–369； UniProt 1–369

PbTRAP

OrganismNot specified

UniProt P90573

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain H； UniProt 601–606	Fragment：C-terminus: Residues 601-606	Fructose-bisphosphate aldolase × 4 （P14223）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5 mM TRAP-tail, 0.5% n-dodecyl-beta-D-maltoside, 50 mM cacodylic acid pH 6.0, 20% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.250

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 2EPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PC4 Crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP-tail determined at 2.4 angstrom resolution Deposited 2007-03-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 601–606（6 aa） Fragment：C-terminus: Residues 601-606	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5 mM TRAP-tail, 0.5% n-dodecyl-beta-D-maltoside, 50 mM Cacodylic acid pH 6.0, 20% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.250

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P90573_PLABE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–6； UniProt 601–606

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	2eph
Deposition date deposition_date	2007-03-30
Structure title title	Crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP-tail determined at 2.7 angstrom resolution
Keywords keywords	;Aldolase, Invasion machinery, Plasmodium falciparum, Structural Genomics, PSI, Protein Structure Initiative, Structural Genomics of Pathogenic Protozoa Consortium, SGPP, 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	35.73 Å
Radius of gyration Rg (electron density) rg_electron	35.02 Å
Forward intensity I(0) i0	354730000.00
Molecular weight molecular_weight	154750.0 kDa
Excluded volume excluded_volume	194970 Å³
Envelope volume envelope_volume	245810 Å³
Hydration-shell volume shell_volume	57005 Å³
Envelope diameter envelope_diameter	127.7 Å
Shell Rg shell_rg	42.36 Å
Envelope Rg envelope_rg	35.78 Å
Shape Rg shape_rg	35.03 Å
Total Rg total_rg	35.47 Å
Total atoms total_atoms	10887
Residues n_residues	1424
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	117.0 Å
Rg (real space) rg_real	35.62 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	3.5470e+08
I(0) uncertainty (real space) i0_real_error	5.6350e+06
Rg (reciprocal space) rg_reciprocal	35.69 Å
I(0) (reciprocal space) i0_reciprocal	354800000.0000
Solution quality estimate total_estimate	0.8911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	68850000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.943

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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	Fructose-bisphosphate aldolase
Molecular weight formula_weight	40152.9 kDa
EC 编号 ec_number	4.1.2.13
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11239

MAHCTEYMNAPKKLPADVAEELATTAQKLVQAGKGILAADESTQTIKKRFDNIKLENTIENRASYRDLLFGTKGLGKFISGAILFEETLFQKNEAGVPMVNLLHNENIIPGIKVDKGLVNIPCTDEEKSTQGLDGLAERCKEYYKAGARFAKWRTVLVIDTAKGKPTDLSIHETAWGLARYASICQQNRLVPIVEPEILADGPHSIEVCAVVTQKVLSCVFKALQENGVLLEGALLKPNMVTAGYECTAKTTTQDVGFLTVRTLRRTVPPALPGVVFLSGGQSEEEASVNLNSINALGPHPWALTFSYGRALQASVLNTWQGKKENVAKAREVLLQRAEANSLATYGKYKGGAGGENAGASLYEKKYVY

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PbTRAP
Molecular weight formula_weight	791.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EDNDWN

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2ephA00
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	2ephB00
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	2ephC00
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	2ephD00
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	70.019 Å
Unit-cell length b length_b	146.162 Å
Unit-cell length c length_c	148.961 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.1945
R_work r_work	0.1915
R_free r_free	0.2504

fit	/app/data/saxs_computation/ep/2eph/2eph.fit
pddf	/app/data/pr_computation/ep/2eph/2eph.pr.out
profile	/app/data/saxs_computation/ep/2eph/2eph.dat

Crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP-tail determined at 2.7 angstrom resolution

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

Fructose-bisphosphate aldolase

State in the Current Structure

Other States of the Same Protein in the Database

PbTRAP

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)