SAXSdb — 6pla

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

Lysozyme

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 19–147	Not recorded	NA SODIUM ION × 1 O1N dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) × 2 OS OSMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Os(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.04 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.25 Å R-free 0.184

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 6PLA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3OTP Crystal structure of the DegP dodecamer with a model substrate Deposited 2010-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain G 36–76（41 aa） Fragment：a model peptide substrate Chain H 36–76（41 aa） Fragment：a model peptide substrate Chain I 36–76（41 aa） Fragment：a model peptide substrate Chain J 36–76（41 aa） Fragment：a model peptide substrate Chain K 36–76（41 aa） Fragment：a model peptide substrate Chain L 36–76（41 aa） Fragment：a model peptide substrate	Mutation：C30S Mutation：C30S Mutation：C30S Mutation：C30S Mutation：C30S Mutation：C30S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；291 K；65 mM citric acid, 35 mM Bis-Tris propane, 8% PEG3350, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K	Resolution 3.76 Å R-free 0.251
5A3Z Structure of monoclinic Lysozyme obtained by multi crystal data collection Deposited 2015-06-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–147（147 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.59 Å R-free 0.265
5A3Z Structure of monoclinic Lysozyme obtained by multi crystal data collection Deposited 2015-06-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–147（147 aa）	Not recorded	NO3 NITRATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.59 Å R-free 0.265
6PBB Crystal structure of Hen Egg White Lysozyme in complex with I3C Deposited 2019-06-13	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	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；289 K；0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350	Resolution 1.89 Å R-free 0.240
6PL9 Adduct formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcyclopentadienyl)rhodium(III) with HEWL Deposited 2019-06-30	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	ORS dichloro[(1,2,3,4,5-eta)-pentamethylcyclopentadienyl]rhodium × 1 R1N 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-rhodapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.09 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.20 Å R-free 0.203
6PLB Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimida zol-2-ylidene)(eta5-pentamethylcyclopentadienyl)iridium(III) with HEWL Deposited 2019-06-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	OT1 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Ir(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(chlorido)2 (1.13 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.30 Å R-free 0.190
6W7P Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment Deposited 2020-03-19	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	NA SODIUM ION × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 4.6；296 K；PEG 6000, NaCl, Na Acetate	Resolution 1.60 Å R-free 0.220
6W8E Crystal Structure Analysis of Space-grown Lysozyme Deposited 2020-03-20	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	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 4.6；296 K；PEG 6000, NaCl, Na Acetate	Resolution 2.68 Å R-free 0.306
6WEB Multi-Hit SFX using MHz XFEL sources Deposited 2020-04-01	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	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 3.5；293 K；NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5	Resolution 2.10 Å R-free 0.216
6WEC Multi-Hit SFX using MHz XFEL sources Deposited 2020-04-01	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	CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 5 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 3.5；293 K；NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5	Resolution 2.10 Å R-free 0.299
6WGO The interaction of dichlorido(3-(anthracen-9-ylmethyl)-1-methylimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL after 1 week Deposited 2020-04-06	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	NA SODIUM ION × 1 ACT ACETATE ION × 2 U0J {(2R)-1-[(anthracen-9-yl)methyl]-3-methyl-2,3-dihydro-1H-imidazol-2-yl}(dichloro)ruthenium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.30 Å R-free 0.192
6WRL The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H-imidazol-3-ide])rhodium(I) with HEWL after 1 week Deposited 2020-04-29	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	NA SODIUM ION × 1 ACT ACETATE ION × 3 RH Rhodium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.35 Å R-free 0.215
6WRM The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H-imidazol-3-ide])rhodium(I) with HEWL after 1 month Deposited 2020-04-29	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	NA SODIUM ION × 1 CL CHLORIDE ION × 2 RH Rhodium × 1 U8G (4-{2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}-1,3-dimethyl-2,3-dihydro-1H-imidazol-2-yl)rhodium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.55 Å R-free 0.249
6WX5 Adducts formed after 3 weeks in the reaction of chlorido[chlorido(2,2'-((2-([2,2':6',2''-Terpyridin]-4'-yloxy)ethyl)azanediyl)bis(ethan-1-ol))platinum(II)] with HEWL Deposited 2020-05-09	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	NA SODIUM ION × 1 ACT ACETATE ION × 1 PT PLATINUM (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride pH 4.7	Resolution 1.30 Å R-free 0.202
7D0W Crystal structure of Hen Egg White Lysozyme Deposited 2020-09-12	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	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298.15 K；PEG 3000, TRIS pH 5.6	Resolution 1.80 Å R-free 0.226

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B8YK79_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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	6pla
Deposition date deposition_date	2019-06-30
Structure title title	Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) with HEWL
Keywords keywords	metal-based, anticancer, ruthenium, NHC, carbene, lysozyme, metallodrug, benzimidazole, dimethylbenzimidazole, HYDROLASE; 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	15.36 Å
Radius of gyration Rg (electron density) rg_electron	14.07 Å
Forward intensity I(0) i0	5719750.00
Molecular weight molecular_weight	15574.0 kDa
Excluded volume excluded_volume	18525 Å³
Envelope volume envelope_volume	20139 Å³
Hydration-shell volume shell_volume	12302 Å³
Envelope diameter envelope_diameter	52.8 Å
Shell Rg shell_rg	19.71 Å
Envelope Rg envelope_rg	14.27 Å
Shape Rg shape_rg	13.98 Å
Total Rg total_rg	15.28 Å
Total atoms total_atoms	1050
Residues n_residues	129
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	51.6 Å
Rg (real space) rg_real	15.28 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	5.7200e+06
I(0) uncertainty (real space) i0_real_error	6.7200e+04
Rg (reciprocal space) rg_reciprocal	15.28 Å
I(0) (reciprocal space) i0_reciprocal	5720000.0000
Solution quality estimate total_estimate	0.6374
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.236
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	690200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 0.999; Sysdev: 0.368; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	Lysozyme
Molecular weight formula_weight	14331.2 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1150

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II)
Molecular weight formula_weight	537.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	OSMIUM ION
Molecular weight formula_weight	190.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6plaa_
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

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8. Citations (1)

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Unit-cell length a length_a	76.448 Å
Unit-cell length b length_b	76.448 Å
Unit-cell length c length_c	37.763 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	34.210 Å
R factor r_factor	0.1521
R_work r_work	0.1505
R_free r_free	0.1836

fit	/app/data/saxs_computation/pl/6pla/6pla.fit
pddf	/app/data/pr_computation/pl/6pla/6pla.pr.out
profile	/app/data/saxs_computation/pl/6pla/6pla.dat

Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) with HEWL

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

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

Diffraction experiment Diffraction