1bu3

REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.

Method: X-RAY DIFFRACTION D_max: 47.7 Å Quality: GOOD

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

CALCIUM-BINDING PROTEIN

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–108	Fragment：CALCIUM-BINDING DOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.00	Resolution 1.65 Å R-free 0.251

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PRVB_MERBI
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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bu3
Deposition date deposition_date	1998-08-30
Structure title title	REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.
Keywords keywords	CALCIUM BINDING; CALCIUM BINDING
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	14.42 Å
Radius of gyration Rg (electron density) rg_electron	12.88 Å
Forward intensity I(0) i0	2562110.00
Molecular weight molecular_weight	11433.0 kDa
Excluded volume excluded_volume	14449 Å³
Envelope volume envelope_volume	16083 Å³
Hydration-shell volume shell_volume	10745 Å³
Envelope diameter envelope_diameter	46.7 Å
Shell Rg shell_rg	18.53 Å
Envelope Rg envelope_rg	13.23 Å
Shape Rg shape_rg	12.85 Å
Total Rg total_rg	14.30 Å
Total atoms total_atoms	805
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

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

Maximum dimension Dmax dmax	47.7 Å
Rg (real space) rg_real	14.31 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.5620e+06
I(0) uncertainty (real space) i0_real_error	2.9080e+04
Rg (reciprocal space) rg_reciprocal	14.32 Å
I(0) (reciprocal space) i0_reciprocal	2562000.0000
Solution quality estimate total_estimate	0.8579
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.035
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	281800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bu3a_
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	1bu3A00
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	75.710 Å
Unit-cell length b length_b	80.730 Å
Unit-cell length c length_c	42.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2510

Description description	CALCIUM-BINDING PROTEIN
Molecular weight formula_weight	11354.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	919

REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.

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

CALCIUM-BINDING PROTEIN

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

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 (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

fit	/app/data/saxs_computation/bu/1bu3/1bu3.fit
pddf	/app/data/pr_computation/bu/1bu3/1bu3.pr.out
profile	/app/data/saxs_computation/bu/1bu3/1bu3.dat