SAXSdb — 3u0k

▼

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

RCaMP

Entacmaea quadricolor

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 204–432 Chain B； UniProt 1–203	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.239

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 3U0K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IK1 High resolution structure of GCaMPJ at pH 8.5 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–48（48 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T, D362Y Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T, D362Y Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；Tris pH 8.5, (NH4)2SO4, 25% PEG 3350, 0.5% DDAO, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.205
4IK3 High resolution structure of GCaMP3 at pH 8.5 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–48（48 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；Tris pH 8.5, (NH4)2SO4, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.01 Å R-free 0.214
4IK4 High resolution structure of GCaMP3 at pH 5.0 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–48（48 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；Bis-Tris pH 5.0, (NH4)2SO4 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.01 Å R-free 0.212
4IK5 High resolution structure of Delta-REST-GCaMP3 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–48（24 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；Tris pH 8.5, NH4OAc, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.228
4IK8 High resolution structure of GCaMP3 dimer form 1 at pH 7.5 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–48（48 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；HEPES pH 7.5, (NH4)2SO4, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.55 Å R-free 0.209
4IK9 High resolution structure of GCaMP3 dimer form 2 at pH 7.5 Deposited 2012-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–48（48 aa） Chain A 284–432（149 aa）	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；HEPES pH 7.5, (NH4)2SO4, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.80 Å R-free 0.195
6ZSM Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in the ON state (non-illuminated) Deposited 2020-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–432（149 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5 FMT FORMIC ACID × 14 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.20 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 19% (w/v) PEG 3350	Resolution 1.95 Å R-free 0.198
6ZSN Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in the OFF state (illuminated) Deposited 2020-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–432（149 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FMT FORMIC ACID × 6 CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.20 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 19% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.259

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

View Construct and Data Evidence

UniProt name	K4DIE3_ENTQU
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain B； PDBConstruct 11–213； UniProt 1–203 Author chain A； PDBConstruct 1–227； UniProt 204–432

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3u0k
Deposition date deposition_date	2011-09-28
Structure title title	Crystal Structure of the genetically encoded calcium indicator RCaMP
Keywords keywords	Fluorescent protein, calcium binding, EF-hand, genetically encoded calcium indicator; FLUORESCENT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.00 Å
Radius of gyration Rg (electron density) rg_electron	24.18 Å
Forward intensity I(0) i0	36260300.00
Molecular weight molecular_weight	44802.0 kDa
Excluded volume excluded_volume	55354 Å³
Envelope volume envelope_volume	67238 Å³
Hydration-shell volume shell_volume	24081 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	30.29 Å
Envelope Rg envelope_rg	24.30 Å
Shape Rg shape_rg	24.15 Å
Total Rg total_rg	24.99 Å
Total atoms total_atoms	3132
Residues n_residues	396
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.7 Å
Rg (real space) rg_real	25.10 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	3.6260e+07
I(0) uncertainty (real space) i0_real_error	4.9720e+05
Rg (reciprocal space) rg_reciprocal	25.08 Å
I(0) (reciprocal space) i0_reciprocal	36260000.0000
Solution quality estimate total_estimate	0.8840
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12900000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.916; Smooth: 0.954

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RCaMP
Molecular weight formula_weight	23279.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	3302

MGSHHHHHHGMASMTGGQQMGRDLYDDDDKDLATMVDSSRRKWNKTGHAVRAIGRLSSAINTEMMYPADGGLRGYTHMALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHYVSHRLERLEESDNEMFVVQREHAVAKFVGLGGGGGTGGSMNSLIKENMRMKVVLEGSVNGHQFKCTGEGEGNPYMGTQTMRIKVIEGGPLPFAFDILATSF

来源 Source

来源生物 organism	Entacmaea quadricolor
通用名 common_name	Bubble-tip anemone
NCBI Class编号 ncbi_taxonomy_id	6118
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RCaMP
Molecular weight formula_weight	26048.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

XSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGVITVMQDTSLEDGCLVYHAQVRGVNFPSNGAVMQKKTKGWEPTRDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLIMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Entacmaea quadricolor
通用名 common_name	Bubble-tip anemone
NCBI Class编号 ncbi_taxonomy_id	6118
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

▶

8. Citations (1)

▶

Unit-cell length a length_a	75.918 Å
Unit-cell length b length_b	75.918 Å
Unit-cell length c length_c	123.161 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	2.100 Å
Low-resolution limit resolution_low	21.580 Å
R factor r_factor	0.1918
R_work r_work	0.1893
R_free r_free	0.2385

fit	/app/data/saxs_computation/u0/3u0k/3u0k.fit
pddf	/app/data/pr_computation/u0/3u0k/3u0k.pr.out
profile	/app/data/saxs_computation/u0/3u0k/3u0k.dat

Crystal Structure of the genetically encoded calcium indicator RCaMP

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

RCaMP

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

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)