SAXSdb — 3kph

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

Superantigen

Mycoplasma arthritidis

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 26–237 Chain B； UniProt 26–237	Fragment：UNP residues 26-239 Mutation：K201A	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.2；293 K；13-15% PEG 3350, 0.2 M NaCl, 5% Ethylene glycol, 5% Glycerol, 0.1 M Potassium/sodium phosphate pH 6.2, VAPOR DIFFUSION, temperature 293K	Resolution 2.80 Å R-free 0.299

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 3KPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1R5I Crystal structure of the MAM-MHC complex Deposited 2003-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 23–238（216 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；potassium sodium hosphate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.246
1R5I Crystal structure of the MAM-MHC complex Deposited 2003-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 23–238（216 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；potassium sodium hosphate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.246
2ICW Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule Deposited 2006-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 26–238（213 aa） Fragment：residues 26-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；298 K；13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K	Resolution 2.41 Å R-free 0.288
2ICW Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule Deposited 2006-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 26–238（213 aa） Fragment：residues 26-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；298 K；13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K	Resolution 2.41 Å R-free 0.288
2OJE Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA Deposited 2007-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 25–238（214 aa） Fragment：residues 25-238	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；1.7M potassium sodium phosphate, 0.1M HEPES, 2 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.261
2OJE Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA Deposited 2007-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 25–238（214 aa） Fragment：residues 25-238	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；1.7M potassium sodium phosphate, 0.1M HEPES, 2 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.261
2OJE Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA Deposited 2007-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 25–238（214 aa） Fragment：residues 25-238 Chain H 25–238（214 aa） Fragment：residues 25-238	Not recorded	PO4 PHOSPHATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；1.7M potassium sodium phosphate, 0.1M HEPES, 2 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.261
8VSJ Engineered peptide-specific binder in complex with HLA-DR1/CLIP Deposited 2024-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 26–149（124 aa）	Mutation：V30C, Q37S, K38I, H39Y, F40L, V41A, Y59D, L72K, L75E, G86D, V88I, D90K, N92G, G93D, delta 94-97, I100V, T110I, I127T, S144C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.28 Å

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q48898_MYCAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–217； UniProt 26–237 Author chain B； PDBConstruct 6–217； UniProt 26–237

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	3kph
Deposition date deposition_date	2009-11-16
Structure title title	Crystal structure of Mycoplasma arthritidis-derived mitogen
Keywords keywords	superantigen, MAM, 3D-domain swap, IMMUNE SYSTEM; IMMUNE SYSTEM
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	29.60 Å
Radius of gyration Rg (electron density) rg_electron	29.77 Å
Forward intensity I(0) i0	32656000.00
Molecular weight molecular_weight	46416.0 kDa
Excluded volume excluded_volume	58948 Å³
Envelope volume envelope_volume	73727 Å³
Hydration-shell volume shell_volume	23938 Å³
Envelope diameter envelope_diameter	119.3 Å
Shell Rg shell_rg	31.65 Å
Envelope Rg envelope_rg	30.30 Å
Shape Rg shape_rg	29.72 Å
Total Rg total_rg	30.11 Å
Total atoms total_atoms	3274
Residues n_residues	390
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	114.0 Å
Rg (real space) rg_real	30.13 Å
Rg uncertainty (real space) rg_real_error	1.98 Å
I(0) (real space) i0_real	3.2660e+07
I(0) uncertainty (real space) i0_real_error	6.6480e+05
Rg (reciprocal space) rg_reciprocal	29.90 Å
I(0) (reciprocal space) i0_reciprocal	32650000.0000
Solution quality estimate total_estimate	0.5616
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.793
Kurtosis Kurtosis kurtosis	0.354
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6241000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.469; Stabil: 0.999; Sysdev: 0.218; Positv: 1.000; Valcen: 0.378; Smooth: 0.861

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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	Superantigen
Molecular weight formula_weight	25570.6 kDa
Mutation mutation	K201A
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	3336

GPLGSMKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELATTSDFAKAVFE

来源 Source

来源生物 organism	Mycoplasma arthritidis
NCBI Class编号 ncbi_taxonomy_id	2111
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3kpha_
Class class	a — All alpha proteins
Fold Fold fold	a.202 — Superantigen MAM
Superfamily Superfamily superfamily	a.202.1 — Superantigen MAM
Family Family family	a.202.1.1 — Superantigen MAM

Domain ID domain_id	d3kphb_
Class class	a — All alpha proteins
Fold Fold fold	a.202 — Superantigen MAM
Superfamily Superfamily superfamily	a.202.1 — Superantigen MAM
Family Family family	a.202.1.1 — Superantigen MAM

CATH v4.4 (4 domains)

Domain ID domain_id	3kphA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1

Domain ID domain_id	3kphA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	530 — mam-mhc complex, Chain D, Domain 2

Domain ID domain_id	3kphB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1

Domain ID domain_id	3kphB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	530 — mam-mhc complex, Chain D, Domain 2

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8. Citations (1)

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Unit-cell length a length_a	181.865 Å
Unit-cell length b length_b	181.865 Å
Unit-cell length c length_c	181.865 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	48

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2530
R_work r_work	0.2530
R_free r_free	0.2990

fit	/app/data/saxs_computation/kp/3kph/3kph.fit
pddf	/app/data/pr_computation/kp/3kph/3kph.pr.out
profile	/app/data/saxs_computation/kp/3kph/3kph.dat

Crystal structure of Mycoplasma arthritidis-derived mitogen

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

Superantigen

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