SAXSdb — 3qkg

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

Protein AMBP

Homo sapiens

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 20–202	Fragment：lipocalin Mutation：C34S	NI NICKEL (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM Tris-HCl, 1.1 M sodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.260

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 3QKG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BIK X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX Deposited 1997-11-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 206–352（147 aa） Fragment：DOMAIN II,78 - 133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.253
4ES7 crystal structure of protein HC from Homo sapiens at 2 angstrom Deposited 2012-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–193（167 aa） Fragment：UNP residues 27-193	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；0.2M ammonium citrate, 20% PEG 3350, 0.1M HEPES pH 6.9, 40% 1,1,1,3,3,3-Hexafluoro-z-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.261
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
6EJ7 Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa）	Mutation：S215A, L220G, V221G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 9 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus precipitant mix 2 (PEG8000 and ethylene glycol), 0.1M Bicine/Tris buffer at pH 7.5 0.1 M of Morpheus NPS mix.	Resolution 2.00 Å R-free 0.230
6EJ8 Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa）	Mutation：L220G, V221G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 2.09 Å R-free 0.223
6EJ9 Human Xylosyltransferase 1 in complex with peptide QEPEGSGGGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–220（11 aa）	Mutation：E212P, L220G, V221G	PO4 PHOSPHATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 2.02 Å R-free 0.225
6EJA Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G214Y, L220G, V221G	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 1.94 Å R-free 0.212
6EJB Human Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa）	Mutation：G216A, L220G, V221G	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 2.56 Å R-free 0.280
6EJC Human Xylosyltransferase 1 in complex with peptide QEEEGSGVGQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G217V, L220G, V221G	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 2.06 Å R-free 0.273
6EJD Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G218P, L220G, V221G	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)	Resolution 2.68 Å R-free 0.279

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

View Construct and Data Evidence

UniProt name	AMBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 20–202

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	3qkg
Deposition date deposition_date	2011-02-01
Structure title title	Crystal structure of alpha-1-microglobulin at 2.3 A resolution
Keywords keywords	Beta barrel, binding protein, Bound chromophore, Human plasma, 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	16.89 Å
Radius of gyration Rg (electron density) rg_electron	15.47 Å
Forward intensity I(0) i0	6875160.00
Molecular weight molecular_weight	18860.0 kDa
Excluded volume excluded_volume	23539 Å³
Envelope volume envelope_volume	27729 Å³
Hydration-shell volume shell_volume	14981 Å³
Envelope diameter envelope_diameter	48.2 Å
Shell Rg shell_rg	21.49 Å
Envelope Rg envelope_rg	15.59 Å
Shape Rg shape_rg	15.45 Å
Total Rg total_rg	16.63 Å
Total atoms total_atoms	1324
Residues n_residues	164
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	49.5 Å
Rg (real space) rg_real	16.75 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	6.8750e+06
I(0) uncertainty (real space) i0_real_error	7.0290e+04
Rg (reciprocal space) rg_reciprocal	16.76 Å
I(0) (reciprocal space) i0_reciprocal	6875000.0000
Solution quality estimate total_estimate	0.9075
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.8 Å
Skewness Skewness skewness	-0.017
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1335000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein AMBP
Molecular weight formula_weight	21956.8 kDa
Mutation mutation	C34S
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	1371

GPVPTPPDNIQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSIFTMADRGECVPGEQEPEPILIPRSAWSHPQFEK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3qkga_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3qkgA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	66.721 Å
Unit-cell length b length_b	66.721 Å
Unit-cell length c length_c	80.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.890 Å
R factor r_factor	0.2148
R_work r_work	0.2126
R_free r_free	0.2595

fit	/app/data/saxs_computation/qk/3qkg/3qkg.fit
pddf	/app/data/pr_computation/qk/3qkg/3qkg.pr.out
profile	/app/data/saxs_computation/qk/3qkg/3qkg.dat

Crystal structure of alpha-1-microglobulin at 2.3 A resolution

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

Protein AMBP

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