SAXSdb — 28qn

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

Maltodextrin-binding protein

Methanosarcina mazei

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–374	Not recorded	DARPin × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 Å

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 28QN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric	Chain V 1–383（383 aa）	Not recorded	MG MAGNESIUM ION × 86 K POTASSIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GFJ Structure of RIP2 CARD domain fused to crystallisable MBP tag Deposited 2018-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–371（371 aa） Chain B 1–371（371 aa） Chain C 1–371（371 aa） Chain D 1–371（371 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M NaNO3, and 22% (w/v) PEG 3350	Resolution 3.30 Å R-free 0.266
6XDS Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol Deposited 2020-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–368（367 aa）	Not recorded	V5S 2-[(4-bromophenyl)amino]ethan-1-ol × 1 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；100 mM BisTris pH 5.5, 100 mM ammonium acetate, 15% PEG4000, 15% glycerol	Resolution 1.47 Å R-free 0.208
8GKH Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with omega RNA and target DNA Deposited 2023-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric	Chain P 1–369（369 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.70 Å

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

View Construct and Data Evidence

UniProt name	A0A0F8NYV9_METMZ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–374； UniProt 1–374

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	28qn
Deposition date deposition_date	2026-02-13
Structure title title	MBP-maltose bound to distal DARPin (AHIR dodecamer scaffold system)
Keywords keywords	MBP, DARPin, scaffold, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.31 Å
Radius of gyration Rg (electron density) rg_electron	26.65 Å
Forward intensity I(0) i0	53043100.00
Molecular weight molecular_weight	57635.0 kDa
Excluded volume excluded_volume	72510 Å³
Envelope volume envelope_volume	89379 Å³
Hydration-shell volume shell_volume	29005 Å³
Envelope diameter envelope_diameter	96.1 Å
Shell Rg shell_rg	33.14 Å
Envelope Rg envelope_rg	26.75 Å
Shape Rg shape_rg	26.63 Å
Total Rg total_rg	27.43 Å
Total atoms total_atoms	4076
Residues n_residues	534
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	94.9 Å
Rg (real space) rg_real	27.40 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	5.3040e+07
I(0) uncertainty (real space) i0_real_error	6.8750e+05
Rg (reciprocal space) rg_reciprocal	27.38 Å
I(0) (reciprocal space) i0_reciprocal	53040000.0000
Solution quality estimate total_estimate	0.8639
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.460
Kurtosis Kurtosis kurtosis	-0.258
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	14930000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.990

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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	DARPin
Molecular weight formula_weight	17244.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4084

ADLGRKLLEAARAGQDDEVRILMANGADVNAADNTGTTPLHLAAYSGHLEIVEVLLKHGADVDASDVFGYTPLHLAAYWGHLEIVEVLLKNGADVNAMDSDGMTPLHLAAKWGYLEIVEVLLKHGADVNAQDKFGKTPKDLARDNGNQWIYELLEAAGRA

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Maltodextrin-binding protein
Molecular weight formula_weight	41193.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKIQEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNGSHHHH

来源 Source

来源生物 organism	Methanosarcina mazei
通用名 common_name	Methanosarcina frisia
NCBI Class编号 ncbi_taxonomy_id	2209
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	150405

fit	/app/data/saxs_computation/8q/28qn/28qn.fit
pddf	/app/data/pr_computation/8q/28qn/28qn.pr.out
profile	/app/data/saxs_computation/8q/28qn/28qn.dat

MBP-maltose bound to distal DARPin (AHIR dodecamer scaffold system)

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

Maltodextrin-binding protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)