SAXSdb — 7rj9

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

Vitronectin

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 154–474	Fragment：UNP RESIDUES 154-285, 324-354, 435-474 Mutation：C180S, C215S, delta 286-323, delta 355-434	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES	Resolution 1.70 Å R-free 0.210
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 154–474	Fragment：UNP RESIDUES 154-285, 324-354, 435-474 Mutation：C180S, C215S, delta 286-323, delta 355-434	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES	Resolution 1.70 Å R-free 0.210

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 7RJ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OC0 plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin Deposited 2003-02-03	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 20–70（51 aa） Fragment：SOMATOMEDIN B, RESIDUES 20-70	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；10MM NAOAC, 50MM NACL, 2-9% PEG12000,25% PEG400, 50MM HEPES, PH 7.4	Resolution 2.28 Å R-free 0.252
1S4G Somatomedin-B Domain of human plasma vitronectin. Deposited 2004-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–70（51 aa） Fragment：Somatomedin B	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.4；298 K；Ionic strength (raw mmCIF value) low NMR sample composition Isolated from human plasma vitronectin by CNBr cleavage	Resolution not provided
1SSU Structural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin B domain of human vitronectin Deposited 2004-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–70（51 aa） Fragment：somatomedin B domain of human vitronectin	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 180 mM；Pressure 1 NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 180 mM；Pressure 1 NMR sample composition N15-labeled protein 20 mM sodium phosphate pH 7.5 \| 90% H2O/10% D2O NMR sample composition unlabeled protein 20 mM sodium phosphate pH 7.5 \| 90% H2O/10% D2O	Resolution not provided
2JQ8 Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris Deposited 2007-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–66（47 aa） Fragment：sequence database residues 20-66	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] SMB, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM SMB, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3BT1 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–60（40 aa） Fragment：sometomedin-B domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.80 Å R-free 0.308
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 21–60（40 aa） Fragment：sometomedin-B domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.50 Å R-free 0.272
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–60（40 aa） Fragment：sometomedin-B domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.50 Å R-free 0.272
4K24 Structure of anti-uPAR Fab ATN-658 in complex with uPAR Deposited 2013-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 21–60（40 aa） Fragment：UNP residues 21-60	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K	Resolution 4.50 Å R-free 0.275
6O5E Crystal structure of the Vitronectin hemopexin-like domain Deposited 2019-03-01	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 154–285（132 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474) Chain A 324–354（31 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474) Chain A 435–474（40 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)	Mutation：C180S, C215S Mutation：C180S, C215S Mutation：C180S, C215S	NA SODIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v PEG1000, 11.25% w/v PEG3350, 3% w/v D-(+)-trehalose]	Resolution 1.90 Å R-free 0.210
6O5E Crystal structure of the Vitronectin hemopexin-like domain Deposited 2019-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 154–285（132 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474) Chain B 324–354（31 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474) Chain B 435–474（40 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)	Mutation：C180S, C215S Mutation：C180S, C215S Mutation：C180S, C215S	NA SODIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 2 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v PEG1000, 11.25% w/v PEG3350, 3% w/v D-(+)-trehalose]	Resolution 1.90 Å R-free 0.210

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

View Construct and Data Evidence

UniProt name	VTNC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–204； UniProt 154–474 Author chain B； PDBConstruct 2–204； UniProt 154–474

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	7rj9
Deposition date deposition_date	2021-07-20
Structure title title	Crystal structure of the Vitronectin hemopexin-like domain binding Calcium
Keywords keywords	Integrin ligand, homopexin-like domain, beta-propeller, serum protein, cell adhesion, complement pathway inhibitor; CELL ADHESION
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	24.43 Å
Radius of gyration Rg (electron density) rg_electron	23.38 Å
Forward intensity I(0) i0	32914400.00
Molecular weight molecular_weight	44465.0 kDa
Excluded volume excluded_volume	55634 Å³
Envelope volume envelope_volume	67014 Å³
Hydration-shell volume shell_volume	24467 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	29.90 Å
Envelope Rg envelope_rg	23.38 Å
Shape Rg shape_rg	23.39 Å
Total Rg total_rg	24.14 Å
Total atoms total_atoms	3149
Residues n_residues	383
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	79.4 Å
Rg (real space) rg_real	24.47 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.2910e+07
I(0) uncertainty (real space) i0_real_error	4.5990e+05
Rg (reciprocal space) rg_reciprocal	24.46 Å
I(0) (reciprocal space) i0_reciprocal	32910000.0000
Solution quality estimate total_estimate	0.8867
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12710000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.977

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Vitronectin
Molecular weight formula_weight	23436.2 kDa
Mutation mutation	C180S, C215S, delta 286-323, delta 355-434
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	3567

MELCSGKPFDAFTDLKNGSLFAFRGQYSYELDEKAVRPGYPKLIRDVWGIEGPIDAAFTRINSQGKTYLFKGSQYWRFEDGVLDPDYPRNISDGFDGIPDNVDAALALPAHSYSGRERVYFFKGKQYWEYQFQRTSAGTRQPQFISRDWHGVPGQVDAAMAGRISVFFFSGDKYYRVNLRTRRVDTVDPPYPRSIAQYWLGCPA

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	344

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8. Citations (1)

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Unit-cell length a length_a	40.832 Å
Unit-cell length b length_b	125.575 Å
Unit-cell length c length_c	40.883 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	35.690 Å
R factor r_factor	0.1730
R_work r_work	0.1705
R_free r_free	0.2102

fit	/app/data/saxs_computation/rj/7rj9/7rj9.fit
pddf	/app/data/pr_computation/rj/7rj9/7rj9.pr.out
profile	/app/data/saxs_computation/rj/7rj9/7rj9.dat

Crystal structure of the Vitronectin hemopexin-like domain binding Calcium

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

Vitronectin

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