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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

Method: X-RAY DIFFRACTION Dmax: 39.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CALCIUM-BINDING PROTEIN

Bos taurus

UniProt P02633

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 4–78 Not recorded CA CALCIUM ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.30 Å

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 3ICB 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 mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different structure-quality metrics 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 mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics 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 mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 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 ligand/ion 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 ligand/ion 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 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） 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 method Different experimental conditions Different structure-quality metrics 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 method Different experimental conditions Different structure-quality metrics 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 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：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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 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 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 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
1RT0 12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Zn(II) Deposited 2003-12-10 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 57–68（12 aa） Fragment：residues 57-68 (SWS P02632)
Not recorded No recorded non-water small molecule 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
2BCA HIGH-RESOLUTION SOLUTION STRUCTURE OF CALCIUM-LOADED CALBINDIN D9K Deposited 1993-08-18 Different ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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
4ICB PROLINE CIS-TRANS ISOMERS IN CALBINDIN D9K OBSERVED BY X-RAY CRYSTALLOGRAPHY Deposited 1991-08-27 Different ligand/ion 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 1–75； UniProt 4–78

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 3icb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3icb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3icb
Deposition date deposition_date1986-09-09
Structure title titleTHE 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
Keywords keywordsCALCIUM-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_guinier13.05 Å
Radius of gyration Rg (electron density) rg_electron11.32 Å
Forward intensity I(0) i01573440.00
Molecular weight molecular_weight8670.0 kDa
Excluded volume excluded_volume10943 ų
Envelope volume envelope_volume11822 ų
Hydration-shell volume shell_volume9036 ų
Envelope diameter envelope_diameter35.0 Å
Shell Rg shell_rg16.78 Å
Envelope Rg envelope_rg11.54 Å
Shape Rg shape_rg11.29 Å
Total Rg total_rg12.81 Å
Total atoms total_atoms607
Residues n_residues75
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 dmax39.5 Å
Rg (real space) rg_real12.93 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real1.5730e+06
I(0) uncertainty (real space) i0_real_error1.4890e+04
Rg (reciprocal space) rg_reciprocal12.93 Å
I(0) (reciprocal space) i0_reciprocal1573000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.5 Å
Skewness Skewness skewness-0.048
Kurtosis Kurtosis kurtosis-0.406
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3icba_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.1 — Calbindin D9K

CATH v4.4 (1 domains)

Domain ID domain_id3icbA00
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 (4)

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9. Files and Curves (10)