SAXSdb — 1jtp

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

LYSOZYME C

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 19–147	Fragment：ENZYME	Single-Domain Antibody × 1 NA SODIUM ION × 3 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；2M Na Formate, 100mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.229
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 19–147	Fragment：ENZYME	Single-Domain Antibody × 1 NA SODIUM ION × 2 FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；2M Na Formate, 100mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.229

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 1JTP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
135L X-RAY STRUCTURE OF MONOCLINIC TURKEY EGG LYSOZYME AT 1.3 ANGSTROMS RESOLUTION Deposited 1993-06-10	Different construct 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 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.30 Å
1DZB Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme Deposited 2000-02-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000	Resolution 2.00 Å R-free 0.306
1DZB Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme Deposited 2000-02-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000	Resolution 2.00 Å R-free 0.306
1JEF TURKEY LYSOZYME COMPLEX WITH (GLCNAC)3 Deposited 1997-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；2.2M AMMONIUM SULFATE, 10% 1-PROPANOL, PH4.2 1.5% PROTEIN, 2MM (GLCNAC)3	Resolution 1.77 Å R-free 0.225
1JSE FULL-MATRIX LEAST-SQUARES REFINEMENT OF TURKEY LYSOZYME Deposited 1998-01-05	Different construct 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 19–147（129 aa）	Not recorded	POL N-PROPANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；2.2M AMMONIUM SULFATE SOLUTION AT PH 4.2 CONTAINING 10% 1-PROPANOL AND 4% PROTEIN	Resolution 1.12 Å R-free 0.140
1LJN Crystal Structure of Turkey Egg Lysozyme Complex with Di-N-acetylchitobiose at 1.19A Resolution Deposited 2002-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；ammonium sulfate, pH 4.2, VAPOR DIFFUSION, temperature 293K	Resolution 1.19 Å R-free 0.138
1LZ2 CRYSTALLOGRAPHIC STUDY OF TURKEY EGG-WHITE LYSOZYME AND ITS COMPLEX WITH A DISACCHARIDE Deposited 1981-09-21	Different construct 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 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1LZY X-RAY STRUCTURE OF TURKEY EGG LYSOZYME COMPLEX WITH DI-N-ACETYLCHITOBIOSE. RECOGNITION AND BINDING OF ALPHA-ANOMERIC FORM Deposited 1995-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1TEW STRUCTURE OF HEXAGONAL TURKEY EGG WHITE LYSOZYME AT 1.65 ANGSTROMS RESOLUTION Deposited 1994-11-17	Different construct 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 19–147（129 aa）	Not recorded	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å
1UAC Crystal Structure of HYHEL-10 FV MUTANT SFSF Complexed with TURKEY WHITE LYSOZYME Deposited 2003-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；PEG 4000, ETHYLENE GLYCOL, AMMONIUM ACETATE, TRI-SODIUM CITRATE DEHYDRATE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.70 Å R-free 0.248
1XFT Synchrotron X-ray Powder Diffraction Study of Hexagonal Turkey Egg-white Lysozyme Deposited 2004-09-15	Different construct Different oligomeric state 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 19–147（129 aa） Fragment：LYSOZYME	Not recorded	No recorded non-water small molecule	POWDER DIFFRACTION X-ray crystallization conditions SALTING OUT；pH 6；295 K；NaCl, pH 6, SALTING OUT, temperature 295K	Resolution 3.35 Å
2LZ2 THE THREE DIMENSIONAL STRUCTURE OF TURKEY EGG WHITE LYSOZYME AT 2.2 ANGSTROMS RESOLUTION Deposited 1988-10-20	Different construct 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 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
3LZ2 STRUCTURE DETERMINATION OF TURKEY EGG WHITE LYSOZYME USING LAUE DIFFRACTION Deposited 1991-09-13	Different construct 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 19–147（129 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LYSC_MELGA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–129； UniProt 19–147 Author chain M； PDBConstruct 1–129； UniProt 19–147

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	1jtp
Deposition date deposition_date	2001-08-21
Structure title title	Degenerate interfaces in antigen-antibody complexes
Keywords keywords	immunoglobulin, heavy chain antibody, VHH, interface, Antibody, Hydrolase; Antibody, Hydrolase
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	29.46 Å
Radius of gyration Rg (electron density) rg_electron	28.97 Å
Forward intensity I(0) i0	58746800.00
Molecular weight molecular_weight	56983.0 kDa
Excluded volume excluded_volume	69729 Å³
Envelope volume envelope_volume	89716 Å³
Hydration-shell volume shell_volume	26669 Å³
Envelope diameter envelope_diameter	98.2 Å
Shell Rg shell_rg	35.20 Å
Envelope Rg envelope_rg	28.90 Å
Shape Rg shape_rg	28.95 Å
Total Rg total_rg	29.56 Å
Total atoms total_atoms	3988
Residues n_residues	526
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	95.0 Å
Rg (real space) rg_real	29.52 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	5.8750e+07
I(0) uncertainty (real space) i0_real_error	8.1500e+05
Rg (reciprocal space) rg_reciprocal	29.50 Å
I(0) (reciprocal space) i0_reciprocal	58750000.0000
Solution quality estimate total_estimate	0.8859
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.7 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.554
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12410000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.822

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Single-Domain Antibody
Molecular weight formula_weight	15757.2 kDa
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	4329

DVQLQASGGGSVQAGGSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAKNTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSSRRYPYDVPDYGSGRA

来源 Source

来源生物 organism	Camelus dromedarius
通用名 common_name	Arabian camel
NCBI Class编号 ncbi_taxonomy_id	9838
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LYSOZYME C
Molecular weight formula_weight	14228.1 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1jtpa_
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	d1jtpb_
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	d1jtpl_
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

Domain ID domain_id	d1jtpm_
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 (4 domains)

Domain ID domain_id	1jtpA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1jtpB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1jtpL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jtpM00
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 (2)

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Unit-cell length a length_a	67.123 Å
Unit-cell length b length_b	69.375 Å
Unit-cell length c length_c	113.231 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	17.000 Å
R factor r_factor	—
R_work r_work	0.1841
R_free r_free	0.2287

fit	/app/data/saxs_computation/jt/1jtp/1jtp.fit
pddf	/app/data/pr_computation/jt/1jtp/1jtp.pr.out
profile	/app/data/saxs_computation/jt/1jtp/1jtp.dat

Degenerate interfaces in antigen-antibody complexes

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

LYSOZYME C

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)