SAXSdb — 2v53

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

SPARC

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	Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 70–212 Chain A； UniProt 221–303	Fragment：FS AND EC DOMAINS, RESIDUES 70-212,221-303	COLLAGEN ALPHA-1(III) CHAIN × 3 （P02461） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 3.20 Å R-free 0.320

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 2V53	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMO BM-40, FS/EC DOMAIN PAIR Deposited 1997-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 71–303（233 aa） Fragment：FS/EC DOMAIN PAIR, RESIDUES 53 - 286 Chain B 71–303（233 aa） Fragment：FS/EC DOMAIN PAIR, RESIDUES 53 - 286	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT 20 DEG C: 10 MG/ML PROTEIN IN 10 MM TRIS PH 7.5 + 2 MM CACL2; 0.1 M HEPES PH 7.5, 0.15 M NA-ACETATE, 15% PEG4K, vapor diffusion - hanging drop	Resolution 3.10 Å R-free 0.322
1NUB HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR Deposited 1997-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 71–303（233 aa） Fragment：FS-EC DOMAIN PAIR, FS, FOLLISTATIN-LIKE, EC, EXTRACELLULAR CALCIUM-BINDING	Mutation：DEL(1-52, 196-203)	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2-PROPANOL., vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.306
1NUB HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR Deposited 1997-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 71–303（233 aa） Fragment：FS-EC DOMAIN PAIR, FS, FOLLISTATIN-LIKE, EC, EXTRACELLULAR CALCIUM-BINDING	Mutation：DEL(1-52, 196-203)	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2-PROPANOL., vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.306
1SRA STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN Deposited 1995-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–303（151 aa） Fragment：CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286)	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.249

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

View Construct and Data Evidence

UniProt name	SPRC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–147； UniProt 70–212 Author chain A； PDBConstruct 148–230； UniProt 221–303

COLLAGEN ALPHA-1(III) CHAIN

OrganismNot specified

UniProt P02461

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 × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 564–584 Chain C； UniProt 564–584 Chain D； UniProt 564–584	Fragment：RESIDUES 564-584 Non-standard monomer：Yes (specific site not provided by mmCIF)	SPARC × 1 （P09486） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 3.20 Å R-free 0.320

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 2V53	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DMW Crystal structure of human type III collagen G982-G1023 containing C-terminal cystine knot Deposited 2008-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1158–1199（42 aa） Fragment：UNP residues 1158-1199 Chain B 1158–1199（42 aa） Fragment：UNP residues 1158-1199 Chain C 1158–1199（42 aa） Fragment：UNP residues 1158-1199	Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q1183M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% PEG 550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.274
4AE2 Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain B 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain C 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466	Mutation：YES Mutation：YES Mutation：YES	CA CALCIUM ION × 3 NO3 NITRATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% PEG 3350, 0.1 M BIS TRIS PROPANE PH 6.5, POTASSIUM NITRATE 0.2 M	Resolution 1.68 Å R-free 0.214
4AEJ Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain B 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Chain C 1222–1466（245 aa） Fragment：CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions 20% PEG 3350, 0.2 M NACL	Resolution 2.21 Å R-free 0.237
4AK3 Crystal structure of Human fibrillar procollagen type III C- propeptide trimer Deposited 2012-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1222–1466（245 aa） Fragment：CPROPEPTIDE, RESIDUES 1222-1466	Mutation：YES	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.337
6FZV Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (short) Deposited 2018-03-15	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 A 1222–1466（245 aa） Chain B 1222–1466（245 aa） Chain C 1222–1466（245 aa）	Not recorded	CA CALCIUM ION × 5 FLC CITRATE ANION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M potassium citrate, 16% PEG3350	Resolution 2.70 Å R-free 0.258
6FZW Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (long) Deposited 2018-03-15	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 A 1185–1466（282 aa） Chain B 1185–1466（282 aa） Chain C 1185–1466（282 aa）	Not recorded	CA CALCIUM ION × 5 FLC CITRATE ANION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M ammonium citrate, 18% PEG3350	Resolution 2.78 Å R-free 0.271
7WWR Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 973–1002（30 aa） Chain B 973–1002（30 aa） Chain C 973–1002（30 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MIB pH5.0, 25% PEG 1500	Resolution 1.30 Å R-free 0.194
7WWS Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 976–1002（27 aa） Chain B 976–1002（27 aa） Chain C 976–1002（27 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M MgAc2, 0.1M Na cacodylate pH6.5, 20% PEG 8000	Resolution 1.30 Å R-free 0.158
7XAN Structure of a triple-helix region of human collagen type III from Trautec Deposited 2022-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 922–948（27 aa） Chain B 922–948（27 aa） Chain C 922–948（27 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.04M K phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol	Resolution 1.50 Å R-free 0.200

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CO3A1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–27； UniProt 564–584 Author chain C； PDBConstruct 7–27； UniProt 564–584 Author chain D； PDBConstruct 7–27； UniProt 564–584

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	2v53
Deposition date deposition_date	2008-10-01
Structure title title	Crystal structure of a SPARC-collagen complex
Keywords keywords	;GLYCOSYLATED PROTEIN, CELL ADHESION, GLYCOPROTEIN, IONIC CHANNEL, ION TRANSPORT, COPPER, CALCIUM, SECRETED, COLLAGEN, TRANSPORT, BASEMENT MEMBRANE, EXTRACELLULAR MATRIX ;; 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	24.26 Å
Radius of gyration Rg (electron density) rg_electron	23.73 Å
Forward intensity I(0) i0	20558600.00
Molecular weight molecular_weight	32822.0 kDa
Excluded volume excluded_volume	40263 Å³
Envelope volume envelope_volume	53258 Å³
Hydration-shell volume shell_volume	20420 Å³
Envelope diameter envelope_diameter	101.5 Å
Shell Rg shell_rg	28.20 Å
Envelope Rg envelope_rg	24.03 Å
Shape Rg shape_rg	23.72 Å
Total Rg total_rg	24.31 Å
Total atoms total_atoms	2300
Residues n_residues	293
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	101.6 Å
Rg (real space) rg_real	24.43 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	2.0560e+07
I(0) uncertainty (real space) i0_real_error	3.4490e+05
Rg (reciprocal space) rg_reciprocal	24.39 Å
I(0) (reciprocal space) i0_reciprocal	20560000.0000
Solution quality estimate total_estimate	0.6520
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	0.355
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1426000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.334; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.470; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SPARC
Molecular weight formula_weight	26633.4 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	2300

APLANPCQNHHCKHGKVCELDENNTPMCVCQDPTSCPAPIGEFEKVCSNDNKTFDSSCHFFATKCTLEGTKKGHKLHLDYIGPCKYIPPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTEKQKLRVKKIHENEKRLEAGDHPEKNYNMYIFPVHWQFGQLDQHPIDGYLSHTELAPLRAPLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDIDKDLVI

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	HOMO SAPIENS

Entity 2 Entity 2 polymer

Description description	COLLAGEN ALPHA-1(III) CHAIN
Molecular weight formula_weight	3067.3 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D

GPPGPPGPPGPSGPRGQPGVMGFPGPKGPPGAP

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2v53A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	2v53A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (2)

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Unit-cell length a length_a	89.790 Å
Unit-cell length b length_b	89.790 Å
Unit-cell length c length_c	127.100 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	24

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.842 Å
R factor r_factor	0.2609
R_work r_work	0.2536
R_free r_free	0.3202

fit	/app/data/saxs_computation/v5/2v53/2v53.fit
pddf	/app/data/pr_computation/v5/2v53/2v53.pr.out
profile	/app/data/saxs_computation/v5/2v53/2v53.dat

Crystal structure of a SPARC-collagen complex

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

SPARC

State in the Current Structure

Other States of the Same Protein in the Database

COLLAGEN ALPHA-1(III) CHAIN

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)