SAXSdb — 1b8c

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

PROTEIN (PARVALBUMIN)

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 Chain B； UniProt 1–108	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

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 1B8C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8L Calcium-bound D51A/E101D/F102W Triple Mutant of Beta Carp Parvalbumin Deposited 1999-02-01	Different construct 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 construct 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 construct 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
1CDP 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 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）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
4CPV REFINED CRYSTAL STRUCTURE OF CALCIUM-LIGANDED CARP PARVALBUMIN 4.25 AT 1.5-ANGSTROMS RESOLUTION Deposited 1989-10-18	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）	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 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）	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 1–108； UniProt 1–108 Author chain B； PDBConstruct 1–108； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b8c
Deposition date deposition_date	1999-01-29
Structure title title	PARVALBUMIN
Keywords keywords	CALCIUM BINDING PROTEIN, EF-HAND PROTEINS, PARVALBUMIN, CALCIUM-BINDING; CALCIUM 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	19.29 Å
Radius of gyration Rg (electron density) rg_electron	18.37 Å
Forward intensity I(0) i0	9377770.00
Molecular weight molecular_weight	22872.0 kDa
Excluded volume excluded_volume	28717 Å³
Envelope volume envelope_volume	33736 Å³
Hydration-shell volume shell_volume	15988 Å³
Envelope diameter envelope_diameter	62.4 Å
Shell Rg shell_rg	23.53 Å
Envelope Rg envelope_rg	18.44 Å
Shape Rg shape_rg	18.35 Å
Total Rg total_rg	19.25 Å
Total atoms total_atoms	1614
Residues n_residues	216
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	62.1 Å
Rg (real space) rg_real	19.29 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.3780e+06
I(0) uncertainty (real space) i0_real_error	1.1590e+05
Rg (reciprocal space) rg_reciprocal	19.29 Å
I(0) (reciprocal space) i0_reciprocal	9378000.0000
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	21.9 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.361
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	2099000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PARVALBUMIN)
Molecular weight formula_weight	11431.8 kDa
Mutation mutation	D51A, E101D, F102W
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	1869

AFAGVLNDADIAAALEACKAADSFNHKAFFAKVGLTSKSADDVKKAFAIIAQDKSGFIEEDELKLFLQNFKADARALTDGETKTFLKAGDSDGDGKIGVDDWTALVKA

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
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	255

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b8ca_
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

Domain ID domain_id	d1b8cb_
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 (2 domains)

Domain ID domain_id	1b8cA00
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	1b8cB00
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 (2)

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Unit-cell length a length_a	35.231 Å
Unit-cell length b length_b	50.211 Å
Unit-cell length c length_c	55.374 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1967
R_work r_work	—
R_free r_free	0.3000

fit	/app/data/saxs_computation/b8/1b8c/1b8c.fit
pddf	/app/data/pr_computation/b8/1b8c/1b8c.pr.out
profile	/app/data/saxs_computation/b8/1b8c/1b8c.dat

PARVALBUMIN

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

PROTEIN (PARVALBUMIN)

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