SAXSdb — 1cdp

▼

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

CADMIUM-SUBSTITUTED CALCIUM-BINDING PARVALBUMIN B

Cyprinus carpio

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 1–108	Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 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 1CDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8C PARVALBUMIN Deposited 1999-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–108（108 aa） Chain B 1–108（108 aa）	Mutation：D51A, E101D, F102W Mutation：D51A, E101D, F102W	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；CRYSTALLIZATION CONDITIONS: 40% PEG 4000, 200 MM MGCL2, 50 M PH 7. THE CRYSTALS WERE GROWN AT 4 DEGREES C., pH 7.0	Resolution 2.00 Å R-free 0.300
1B8L Calcium-bound D51A/E101D/F102W Triple Mutant of Beta Carp Parvalbumin Deposited 1999-02-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–108（108 aa）	Mutation：D51A, E101D, F102W	CO3 CARBONATE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.9；CRYSTALLIZATION CONDITIONS 40% PEG 4000, 50 MM CACL2, 50 M PH 7.0, 4 DEGREES C, pH 6.9	Resolution 1.70 Å R-free 0.227
1B8R PARVALBUMIN Deposited 1999-02-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–108（108 aa）	Mutation：F102W	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；CRYSTALLIZATION CONDITIONS: PH 5.0 - 5.5, 3.1 - 3.2 M AMMONIUM SULFATE 0.05 - 0.10 M CACL2, ROOM TEMPERATURE, pH 7.0	Resolution 1.90 Å R-free 0.270
1B9A PARVALBUMIN (MUTATION;D51A, F102W) Deposited 1999-02-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–108（108 aa）	Mutation：D51A, F102W	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.00 Å R-free 0.290
4CPV REFINED CRYSTAL STRUCTURE OF CALCIUM-LIGANDED CARP PARVALBUMIN 4.25 AT 1.5-ANGSTROMS RESOLUTION Deposited 1989-10-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–108（108 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
5CPV RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION Deposited 1990-01-24	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–108（108 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRVB_CYPCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–109； UniProt 1–108

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	1cdp
Deposition date deposition_date	1990-01-24
Structure title title	RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION
Keywords keywords	CALCIUM BINDING; CALCIUM BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.10 Å
Radius of gyration Rg (electron density) rg_electron	12.52 Å
Forward intensity I(0) i0	2903290.00
Molecular weight molecular_weight	11698.0 kDa
Excluded volume excluded_volume	14497 Å³
Envelope volume envelope_volume	15524 Å³
Hydration-shell volume shell_volume	10627 Å³
Envelope diameter envelope_diameter	40.0 Å
Shell Rg shell_rg	18.20 Å
Envelope Rg envelope_rg	12.69 Å
Shape Rg shape_rg	12.46 Å
Total Rg total_rg	13.92 Å
Total atoms total_atoms	812
Residues n_residues	108
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	42.6 Å
Rg (real space) rg_real	13.97 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	2.9030e+06
I(0) uncertainty (real space) i0_real_error	3.1420e+04
Rg (reciprocal space) rg_reciprocal	13.98 Å
I(0) (reciprocal space) i0_reciprocal	2903000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.0 Å
Skewness Skewness skewness	-0.041
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	214200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.936

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CADMIUM-SUBSTITUTED CALCIUM-BINDING PARVALBUMIN B
Molecular weight formula_weight	11476.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	885

XAFAGVLNDADIAAALEACKAADSFNHKAFFAKVGLTSKSADDVKKAFAIIDQDKSGFIEEDELKLFLQNFKADARALTDGETKTFLKAGDSDGDGKIGVDEFTALVKA

来源 Source

来源生物 organism	Cyprinus carpio
通用名 common_name	common carp
NCBI Class编号 ncbi_taxonomy_id	7962

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cdpa_
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.39.1.4 — Parvalbumin

CATH v4.4 (1 domains)

Domain ID domain_id	1cdpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

▶

8. Citations (14)

;Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution. ;

J.Biol.Chem. (1989)

PMID: 2777802 PRIMARY

The Coordination Polyhedron of Ca2+,Cd2+ in Parvalbumin

Inorg.Chim.Acta. (1989)

Refinement of the Structure of Carp Muscle Calcium-Binding Parvalbumin by Model Building and Difference Fourier Analysis

J.Mol.Biol. (1975)

Terbium Replacement of Calcium in Carp Muscle Calcium-Binding Parvalbumin,an X-Ray Crystallographic Study

J.Mol.Biol. (1975)

Troponin and Parvalbumin Calcium Binding Regions Predicted in Myosin Light Chain and T4 Lysozyme

Science (1975)

Calcium Binding Proteins and Natural Membranes

Perspectives in Membrane Biology (1974)

The Coordination of Calcium Ions by Carp Muscle Calcium-Binding Proteins A,B,and C

Adv.Exp.Med.Biol. (1974)

Carp Muscle Calcium-Binding Protein, I.Characterization of the Tryptic Peptides and the Complete Amino Acid Sequence of Component B

J.Biol.Chem. (1973)

Carp Muscle Calcium-Binding Protein, II.Structure Determination and General Description

J.Biol.Chem. (1973)

Carp Muscle Calcium-Binding Protein, III.Phase Refinement Using the Tangent Formula

J.Biol.Chem. (1973)

Gene Duplication in Carp Muscle Calcium Binding Protein

Nature New Biol. (1972)

Gene Triplication Deduced from the Tertiary Structure of a Muscle Calcium Binding Protein

Nature New Biol. (1972)

Structure of a Calcium Binding Carp Myogen

Proc.Natl.Acad.Sci.USA (1972)

The Structure of a Calcium-Binding Protein from Carp Muscle

Cold Spring Harbor Symp.Quant.Biol. (1972)

▶

Unit-cell length a length_a	28.440 Å
Unit-cell length b length_b	60.460 Å
Unit-cell length c length_c	54.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1640
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/cd/1cdp/1cdp.fit
pddf	/app/data/pr_computation/cd/1cdp/1cdp.pr.out
profile	/app/data/saxs_computation/cd/1cdp/1cdp.dat

RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION

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

CADMIUM-SUBSTITUTED CALCIUM-BINDING PARVALBUMIN B

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (14)

9. Files and Curves (10)

Files (7)

Curves (3)