SAXSdb — 1rt0

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

Vitamin D-dependent calcium-binding protein, intestinal

OrganismNot specified

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 57–68	Fragment：residues 57-68 (SWS P02632)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；288 K；Ionic strength (raw mmCIF value) aprox 0；Pressure ambient NMR sample composition：3mM Peptide and Zn(NO3)2. NaOH and HNO3 added for pH fixing to 7; 80% H2O, 20% D2O \| 80% H2O, 20% D2O	Resolution not provided

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 1RT0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B1G SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K Deposited 1998-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Mutation：P43G	CA CALCIUM ION × 2	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1BOC THE SOLUTION STRUCTURES OF MUTANT CALBINDIN D9K'S, AS DETERMINED BY NMR, SHOW THAT THE CALCIUM BINDING SITE CAN ADOPT DIFFERENT FOLDS Deposited 1993-04-23	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1BOD THE SOLUTION STRUCTURES OF MUTANT CALBINDIN D9K'S, AS DETERMINED BY NMR, SHOW THAT THE CALCIUM BINDING SITE CAN ADOPT DIFFERENT FOLDS Deposited 1993-04-23	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Mutation：A15D,P20G,P43M	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CDN Solution structure of (CD2+)1-calbindin D9K reveals details of the stepwise structural changes along the apo--> (CA2+)II1--> (CA2+)I,II2 binding pathway Deposited 1995-08-04	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Mutation：INS(MET 1), P43G	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CLB Determination of the solution structure of apo calbindin D9K by nmr spectroscopy Deposited 1995-02-08	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1D1O COOPERATIVITY IN EF-HAND CA2+-BINDING PROTEINS: EVIDENCE OF SITE-SITE COMMUNICATION FROM BINDING-INDUCED CHANGES IN STRUCTURE AND DYNAMICS OF N56A CALBINDIN D9K Deposited 1999-09-20	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–79（75 aa） Fragment：CALBINDIN D9K	Mutation：P43M, N56A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 4 MM N56A-CALBINDIN D9K NMR sample composition 4 MM 15N-LABELED N56A-CALBINDIN D9K;	Resolution not provided
1HT9 DOMAIN SWAPPING EF-HANDS Deposited 2000-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–78（75 aa） Chain B 4–78（75 aa）	Mutation：YES Mutation：YES	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；ammonium sulphate, calcium chloride, magnesium chloride, EVAPORATION, temperature 293K	Resolution 1.76 Å R-free 0.192
1IG5 BOVINE CALBINDIN D9K BINDING MG2+ Deposited 2001-04-17	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 4–78（75 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.4；298 K；3M ammonium sulphate, 100 mM magnesium chloride, pH 6.4, EVAPORATION, temperature 298K	Resolution 1.50 Å R-free 0.285
1IGV BOVINE CALBINDIN D9K BINDING MN2+ Deposited 2001-04-18	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 4–78（75 aa）	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；295 K；65 % ammonium sulphate, 600 mM MnCl2, pH 5.6, EVAPORATION, temperature 295K	Resolution 1.85 Å R-free 0.272
1KCY NMR solution structure of apo calbindin D9k (F36G + P43M mutant) Deposited 2001-11-12	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa） Fragment：contains EF-HAND 1 (LOW AFFINITY) and EF-HAND 2 (HIGH AFFINITY)	Mutation：F36G, P43M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) no added salts；Pressure ambient NMR sample composition 2.5 mM calbindin; 95% H2O; 5% D2O \| 95% H20; 5% D2O NMR sample composition 2.5 mM calbindin D9k U-15N; 95% H2O; 5% D2O \| 95% H2O/5% D2O NMR sample composition 2.5 mM calbindin D9k; 100% D20 \| 100% D2O	Resolution not provided
1KQV Family of NMR Solution Structures of Ca Ln Calbindin D9K Deposited 2002-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–78（79 aa）	Mutation：P43M	LA LANTHANUM (III) ION × 1	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) water solution；Pressure 1 NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) water solution；Pressure 1 NMR sample composition 2.0 mM Ca Ln Cb \| H2O/D2O 10:1	Resolution not provided
1KSM AVERAGE NMR SOLUTION STRUCTURE OF CA LN CALBINDIN D9K Deposited 2002-01-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–78（79 aa）	Mutation：P43M	LA LANTHANUM (III) ION × 1	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) WATER SOLUTION；Pressure AMBIENT NMR sample composition 1.5 MM [15N, 13C] - CA LN CALBINDIN, PH 6.0 \| H20:D2O 90:10	Resolution not provided
1N65 FAMILY OF NMR SOLUTION STRUCTURES OF CA CE CALBINDIN D9K IN DENATURATING CONDITIONS Deposited 2002-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Mutation：P43M	CE CERIUM (III) ION × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 2M Guanidinium Chloride (GmdHCl)；Pressure 1 NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) pure water；Pressure 1 NMR sample composition Uniform labeling with 15N, H2O/D20 90/10 \| H2O/D20 90/10 Denaturating Conditions NMR sample composition Uniform labeling with 15N, H2O/D20 90/10 \| H2O/D20 90/10	Resolution not provided
1QX2 X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution Deposited 2003-09-04	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 4–78（75 aa）	Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.44 Å R-free 0.194
1QX2 X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution Deposited 2003-09-04	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–78（75 aa）	Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.44 Å R-free 0.194
1QX2 X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution Deposited 2003-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–78（75 aa） Chain B 4–78（75 aa）	Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.44 Å R-free 0.194
1QX2 X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution Deposited 2003-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–78（75 aa） Chain B 4–78（75 aa）	Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.44 Å R-free 0.194
1QX2 X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution Deposited 2003-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–78（75 aa） Chain B 4–78（75 aa）	Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.44 Å R-free 0.194
2BCA HIGH-RESOLUTION SOLUTION STRUCTURE OF CALCIUM-LOADED CALBINDIN D9K Deposited 1993-08-18	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2BCB HIGH-RESOLUTION SOLUTION STRUCTURE OF CALCIUM-LOADED CALBINDIN D9K Deposited 1993-08-18	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–78（75 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2MAZ Backbone 1H, 13C, and 15N Chemical Shift Assignments for Bovine Apo Calbindin Deposited 2013-07-22	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–79（75 aa） Fragment：UNP residues 5-79	Mutation：P43M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1mM [U-100% 13C; U-100% 15N] D2O-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3ICB THE REFINED STRUCTURE OF VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN FROM BOVINE INTESTINE. MOLECULAR DETAILS, ION BINDING, AND IMPLICATIONS FOR THE STRUCTURE OF OTHER CALCIUM-BINDING PROTEINS Deposited 1986-09-09	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 4–78（75 aa）	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
4ICB PROLINE CIS-TRANS ISOMERS IN CALBINDIN D9K OBSERVED BY X-RAY CRYSTALLOGRAPHY Deposited 1991-08-27	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 4–78（75 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å

19 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S100G_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–12； UniProt 57–68

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	1rt0
Deposition date deposition_date	2003-12-10
Structure title title	12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Zn(II)
Keywords keywords	EF-hand toxic metal ion transport model of ICaBP coordination toward zinc, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	4.87 Å
Radius of gyration Rg (electron density) rg_electron	5.47 Å
Forward intensity I(0) i0	3550670.00
Molecular weight molecular_weight	13043.0 kDa
Excluded volume excluded_volume	15287 Å³
Envelope volume envelope_volume	1854 Å³
Hydration-shell volume shell_volume	3101 Å³
Envelope diameter envelope_diameter	19.0 Å
Shell Rg shell_rg	10.25 Å
Envelope Rg envelope_rg	6.23 Å
Shape Rg shape_rg	5.45 Å
Total Rg total_rg	5.88 Å
Total atoms total_atoms	1510
Residues n_residues	120
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	19.4 Å
Rg (real space) rg_real	4.80 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	3.5510e+06
I(0) uncertainty (real space) i0_real_error	3.1680e+04
Rg (reciprocal space) rg_reciprocal	4.80 Å
I(0) (reciprocal space) i0_reciprocal	3551000.0000
Solution quality estimate total_estimate	0.6972
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	7.4 Å
Skewness Skewness skewness	-0.493
Kurtosis Kurtosis kurtosis	-0.600
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	414.4000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.127; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.727

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Vitamin D-dependent calcium-binding protein, intestinal
Molecular weight formula_weight	1326.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1510

fit	/app/data/saxs_computation/rt/1rt0/1rt0.fit
pddf	/app/data/pr_computation/rt/1rt0/1rt0.pr.out
profile	/app/data/saxs_computation/rt/1rt0/1rt0.dat

12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Zn(II)

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

Vitamin D-dependent calcium-binding protein, intestinal

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)