SAXSdb — 3cml

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

Erythrocyte membrane protein 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1220–1580	Fragment：DBL3x domain (UNP residues 1220-1580)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.253

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 3CML	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Y8D STRUCTURE OF DBL6 EPSILON DOMAIN FROM VAR2CSA STRAIN FCR3 Deposited 2011-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2326–2631（306 aa） Fragment：DBL6 EPSILON, RESIDUES 2326-2631	Not recorded	DHL 2-AMINO-ETHANETHIOL × 2 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；30% PEG 4000, 0.1M NA ACETATE, PH 4.8, 0.1M MGCL2, 2.6% BENZAMIDINE, 10MG/ML PROTEIN IN 0.02M TRIS PH 8, 0.14M NACL, 0.045M CYSTAMINE; VAPOUR DIFFUSION	Resolution 1.84 Å R-free 0.235
3BQI Structure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein Deposited 2007-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1218–1577（360 aa） Fragment：DBL3X domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.291
3BQK Structure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein in complex with sulphate Deposited 2007-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1218–1577（360 aa） Fragment：DBL3X domain	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20% PEG 4K, 20mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.286
3BQL Structure of a chondroitin sulphate binding DBL3X domain from a var2csa encoded PfEMP1 protein Deposited 2007-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1218–1577（360 aa） Fragment：DBL3X domain	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 4K, 20mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.271
3CPZ Crystal structure of VAR2CSA DBL3x domain in the presence of dodecasaccharide of CSA Deposited 2008-04-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1220–1580（361 aa） Fragment：DBL3x domain (UNP residues 1220-1580)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 3350, 0.1M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.353
4P1T Crystal structure of the DBL3X-DBL4epsilon double domain from the extracellular part of VAR2CSA PfEMP1 from Plasmodium falciparum Deposited 2014-02-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1215–1950（736 aa） Fragment：DBL3X-DBL4epsilon double domain (UNP residues 1215-1950)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；18% PEG 3000, 100 mM Bis-Tris buffer, 300 mM sodium chloride	Resolution 2.90 Å R-free 0.276
7B52 VAR2CSA full ectodomain Deposited 2020-12-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–2649（2649 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM Tris pH 7.5, 125mM KCl cryo-EM vitrification conditions Cryogen ETHANE；Added 1mM FF8 as additive just before freezing	Resolution 3.80 Å
7B54 VAR2CSA full ectodomain in present of plCS, DBL1-DBL4 Deposited 2020-12-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 500–1985（1486 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM Tris pH 7.5 and 75mM KCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7JGD Cryo-EM structure of P. falciparum VAR2CSA FCR3 core at 3.4 A Deposited 2020-07-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–2649（2649 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
7JGE Cryo-EM structure of P. falciparum VAR2CSA FCR3 core at 4 A Deposited 2020-07-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–2649（2649 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7JGF Cryo-EM structure of P. falciparum VAR2CSA FCR3 domains DBL5 and DBL6 at 4.69 A Deposited 2020-07-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–2649（2649 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.69 Å
7NNH Cryo-EM structure of VAR2CSA FCR3 domain DBL5/6 Deposited 2021-02-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–2649（2649 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM Tris pH 7.5 and 75mM KCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7Y0H Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3 Deposited 2022-06-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain M 1–2628（2628 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6UDW7_PLAFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–362； UniProt 1220–1580

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	3cml
Deposition date deposition_date	2008-03-23
Structure title title	Crystal Structure of the DBL3x domain of the Plasmodium falcipurum VAR2CSA protein
Keywords keywords	DBL3x, VAR2CSA, chondroitin-sulfate binding domain, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	22.10 Å
Radius of gyration Rg (electron density) rg_electron	21.22 Å
Forward intensity I(0) i0	21002500.00
Molecular weight molecular_weight	33593.0 kDa
Excluded volume excluded_volume	41447 Å³
Envelope volume envelope_volume	51057 Å³
Hydration-shell volume shell_volume	20803 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	27.36 Å
Envelope Rg envelope_rg	21.82 Å
Shape Rg shape_rg	21.22 Å
Total Rg total_rg	22.04 Å
Total atoms total_atoms	2367
Residues n_residues	317
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	81.7 Å
Rg (real space) rg_real	22.21 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.1000e+07
I(0) uncertainty (real space) i0_real_error	3.2380e+05
Rg (reciprocal space) rg_reciprocal	22.19 Å
I(0) (reciprocal space) i0_reciprocal	21000000.0000
Solution quality estimate total_estimate	0.8160
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.544
Kurtosis Kurtosis kurtosis	0.113
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6316000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.617; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.985

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3cmlA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	20 — Duffy-antigen binding domain

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8. Citations (1)

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Unit-cell length a length_a	40.670 Å
Unit-cell length b length_b	84.200 Å
Unit-cell length c length_c	86.490 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	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2530

Description description	Erythrocyte membrane protein 1
Molecular weight formula_weight	41460.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2465

Crystal Structure of the DBL3x domain of the Plasmodium falcipurum VAR2CSA protein

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

Erythrocyte membrane protein 1

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite
NCBI Class编号 ncbi_taxonomy_id	5833
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	98

fit	/app/data/saxs_computation/cm/3cml/3cml.fit
pddf	/app/data/pr_computation/cm/3cml/3cml.pr.out
profile	/app/data/saxs_computation/cm/3cml/3cml.dat