SAXSdb — 1y1a

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

Calcium and integrin binding 1 (calmyrin)

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 9–191	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 9–191	Not recorded	CA CALCIUM ION × 3 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 9–191 Chain B； UniProt 9–191	Not recorded	CA CALCIUM ION × 12 GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 9–191 Chain B； UniProt 9–191	Not recorded	CA CALCIUM ION × 6 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 9–191	Not recorded	CA CALCIUM ION × 6 GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251

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 1Y1A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DGU HOMOLOGY-BASED MODEL OF CALCIUM-SATURATED CIB (CALCIUM-AND INTEGRIN-BINDING PROTEIN) Deposited 1999-11-25	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 9–191（183 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1DGV HOMOLOGY-BASED MODEL OF APO CIB (CALCIUM-AND INTEGRIN-BINDING PROTEIN) Deposited 1999-11-25	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 9–191（183 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1XO5 Crystal structure of CIB1, an EF-hand, integrin and kinase-binding protein Deposited 2004-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–190（183 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；20 mM Bis-Tris-propane (BTP), 300 mM calcium acetate, 18% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.99 Å R-free 0.257
1XO5 Crystal structure of CIB1, an EF-hand, integrin and kinase-binding protein Deposited 2004-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 8–190（183 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；20 mM Bis-Tris-propane (BTP), 300 mM calcium acetate, 18% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.99 Å R-free 0.257
2L4H The Solution Structure of Calcium Bound CIB1 Deposited 2010-10-06	Different construct 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 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium cloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM I/L/V methyl 13C and 1H, [U,2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L4I The Solution Structure of Magnesium bound CIB1 Deposited 2010-10-06	Different construct 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 1–191（191 aa）	Not recorded	MG MAGNESIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM I/L/V methyl labeled [U, 2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LM5 Solution structure of Ca2+-CIB1 in complex with the cytoplasmic domain of the integrin aIIb subunit Deposited 2011-11-22	Different construct 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 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-10% 13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 14 mg/mL pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 5 % C12E5/glycerol (0.96/1), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6OCX Structure of human CIB1 in complex with peptide inhibitor UNC10245109 Deposited 2019-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
6OCX Structure of human CIB1 in complex with peptide inhibitor UNC10245109 Deposited 2019-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
6OCX Structure of human CIB1 in complex with peptide inhibitor UNC10245109 Deposited 2019-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
6OCX Structure of human CIB1 in complex with peptide inhibitor UNC10245109 Deposited 2019-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
6OD0 Structure of human CIB1 in complex with peptide inhibitor UNC10245092 Deposited 2019-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；294 K；137.5 mM calcium acetate, 16 % PEG 3350, 20 mM Bis-Tris propane (pH 6.8)	Resolution 2.15 Å R-free 0.229
6OD0 Structure of human CIB1 in complex with peptide inhibitor UNC10245092 Deposited 2019-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–191（191 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；294 K；137.5 mM calcium acetate, 16 % PEG 3350, 20 mM Bis-Tris propane (pH 6.8)	Resolution 2.15 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	KIP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 9–191 Author chain B； PDBConstruct 1–183； UniProt 9–191

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	1y1a
Deposition date deposition_date	2004-11-17
Structure title title	CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN
Keywords keywords	CALCIUM-BINDING PROTEIN, INTEGRIN, EF-HAND, GLUTATHIONE, GLUTATHIOLATION, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	24.40 Å
Radius of gyration Rg (electron density) rg_electron	22.97 Å
Forward intensity I(0) i0	31210500.00
Molecular weight molecular_weight	42435.0 kDa
Excluded volume excluded_volume	52948 Å³
Envelope volume envelope_volume	67253 Å³
Hydration-shell volume shell_volume	24477 Å³
Envelope diameter envelope_diameter	80.0 Å
Shell Rg shell_rg	29.91 Å
Envelope Rg envelope_rg	23.18 Å
Shape Rg shape_rg	22.93 Å
Total Rg total_rg	23.98 Å
Total atoms total_atoms	2978
Residues n_residues	366
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	75.7 Å
Rg (real space) rg_real	24.29 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.1210e+07
I(0) uncertainty (real space) i0_real_error	3.9030e+05
Rg (reciprocal space) rg_reciprocal	24.32 Å
I(0) (reciprocal space) i0_reciprocal	31210000.0000
Solution quality estimate total_estimate	0.8335
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	74.5 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.594
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9321000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	Calcium and integrin binding 1 (calmyrin)
Molecular weight formula_weight	20980.5 kDa
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	3259

SKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTGEGEDTRLSASEMKQLIDNILEESDIDRDGTINLSEFQHVISRSPDFASSFKIVL

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

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	6

Entity 3 Entity 3 non-polymer

Description description	GLUTATHIONE
Molecular weight formula_weight	307.3 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	278

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1y1aa_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d1y1ab_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (4 domains)

Domain ID domain_id	1y1aA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1y1aA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1y1aB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1y1aB02
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 (1)

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Unit-cell length a length_a	115.222 Å
Unit-cell length b length_b	115.222 Å
Unit-cell length c length_c	268.202 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.250 Å
R factor r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2510

fit	/app/data/saxs_computation/y1/1y1a/1y1a.fit
pddf	/app/data/pr_computation/y1/1y1a/1y1a.pr.out
profile	/app/data/saxs_computation/y1/1y1a/1y1a.dat

CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN

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

Calcium and integrin binding 1 (calmyrin)

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