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1sra

STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN

Method: X-RAY DIFFRACTION Dmax: 52.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SPARC

Homo sapiens

UniProt P09486

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 153–303 Fragment：CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286) 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

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 1SRA 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 mutation/modification 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 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 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
2V53 Crystal structure of a SPARC-collagen complex Deposited 2008-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 70–212（143 aa） Fragment：FS AND EC DOMAINS, RESIDUES 70-212,221-303
Chain A 221–303（83 aa） Fragment：FS AND EC DOMAINS, RESIDUES 70-212,221-303
Not recorded 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

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 1–151； UniProt 153–303

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1sra

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1sra
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1sra
Deposition date deposition_date1995-08-21
Structure title titleSTRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN
Keywords keywordsEXTRACELLULAR MATRIX PROTEIN, CALCIUM-BINDING PROTEIN; CALCIUM-BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.82 Å
Radius of gyration Rg (electron density) rg_electron15.44 Å
Forward intensity I(0) i06153280.00
Molecular weight molecular_weight18026.0 kDa
Excluded volume excluded_volume22584 ų
Envelope volume envelope_volume25897 ų
Hydration-shell volume shell_volume14183 ų
Envelope diameter envelope_diameter52.0 Å
Shell Rg shell_rg21.19 Å
Envelope Rg envelope_rg15.69 Å
Shape Rg shape_rg15.41 Å
Total Rg total_rg16.61 Å
Total atoms total_atoms1265
Residues n_residues151
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax52.6 Å
Rg (real space) rg_real16.71 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real6.1530e+06
I(0) uncertainty (real space) i0_real_error6.4930e+04
Rg (reciprocal space) rg_reciprocal16.72 Å
I(0) (reciprocal space) i0_reciprocal6153000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.5 Å
Skewness Skewness skewness0.070
Kurtosis Kurtosis kurtosis-0.460
Angular range angular_range— – 0.4750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha841500.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1sraa_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.3 — Osteonectin

CATH v4.4 (1 domains)

Domain ID domain_id1sraA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (3)

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9. Files and Curves (10)