SAXSdb — 1bql

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

BOBWHITE QUAIL LYSOZYME

Colinus virginianus

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Y； UniProt 1–129	Not recorded	HYHEL-5 FAB (LIGHT CHAIN) × 1 HYHEL-5 FAB (HEAVY CHAIN) × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.60 Å R-free 0.291

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 1BQL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DKJ BOBWHITE QUAIL LYSOZYME Deposited 1996-01-10	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–129（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1DKK BOBWHITE QUAIL LYSOZYME WITH NITRATE Deposited 1996-01-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–129（129 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1DKK BOBWHITE QUAIL LYSOZYME WITH NITRATE Deposited 1996-01-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–129（129 aa）	Not recorded	NO3 NITRATE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LYSC_COLVI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Y； PDBConstruct 1–129； UniProt 1–129

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	1bql
Deposition date deposition_date	1995-02-03
Structure title title	STRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUAIL LYSOZYME
Keywords keywords	ANTIBODY-ANTIGEN complex, HYHEL-5, ANTI-LYSOZYME, BOBWHITE QUAIL; ANTIBODY/ANTIGEN
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	30.60 Å
Radius of gyration Rg (electron density) rg_electron	30.41 Å
Forward intensity I(0) i0	63316600.00
Molecular weight molecular_weight	60402.0 kDa
Excluded volume excluded_volume	74537 Å³
Envelope volume envelope_volume	95915 Å³
Hydration-shell volume shell_volume	28796 Å³
Envelope diameter envelope_diameter	109.9 Å
Shell Rg shell_rg	34.64 Å
Envelope Rg envelope_rg	30.21 Å
Shape Rg shape_rg	30.35 Å
Total Rg total_rg	30.94 Å
Total atoms total_atoms	4240
Residues n_residues	555
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	107.4 Å
Rg (real space) rg_real	30.93 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	6.3320e+07
I(0) uncertainty (real space) i0_real_error	1.0030e+06
Rg (reciprocal space) rg_reciprocal	30.79 Å
I(0) (reciprocal space) i0_reciprocal	63310000.0000
Solution quality estimate total_estimate	0.8241
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	-0.195
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11030000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.669; Smooth: 0.895

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HYHEL-5 FAB (LIGHT CHAIN)
Molecular weight formula_weight	23326.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	4326

DIVLTQSPAIMSASPGEKVTMTCSASSSVNYMYWYQQKSGTSPKRWIYDTSKLASGVPVRFSGSGSGTSYSLTISSMETEDAATYYCQQWGRNPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 2 Entity 2 polymer

Description description	HYHEL-5 FAB (HEAVY CHAIN)
Molecular weight formula_weight	22948.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGAELMKPGASVKISCKASGYTFSDYWIEWVKQRPGHGLEWIGEILPGSGSTNYHERFKGKATFTADTSSSTAYMQLNSLTSEDSGVYYCLHGNYDFDGWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVP

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 3 Entity 3 polymer

Description description	BOBWHITE QUAIL LYSOZYME
Molecular weight formula_weight	14289.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

来源 Source

来源生物 organism	Colinus virginianus
通用名 common_name	northern bobwhite
NCBI Class编号 ncbi_taxonomy_id	9014

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1bqlh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1bqlh2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1bqll1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1bqll2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1bqly_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.2 — C-type lysozyme

CATH v4.4 (5 domains)

Domain ID domain_id	1bqlH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1bqlH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1bqlL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1bqlL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1bqlY00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

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8. Citations (3)

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Unit-cell length a length_a	54.800 Å
Unit-cell length b length_b	74.800 Å
Unit-cell length c length_c	79.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2910

fit	/app/data/saxs_computation/bq/1bql/1bql.fit
pddf	/app/data/pr_computation/bq/1bql/1bql.pr.out
profile	/app/data/saxs_computation/bq/1bql/1bql.dat

STRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUAIL LYSOZYME

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

BOBWHITE QUAIL LYSOZYME

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)