SAXSdb — 9wys

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

Chitin elicitor receptor kinase 1

Oryza sativa Japonica Group

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 303–604 Chain B； UniProt 303–604	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.04 M HEPES sodium pH 7.5, 4% v/v 2-Propanol, 0.02 M Sodium citrate tribasic dihydrate, 2% w/v Polyethylene glycol 3,350, 8% w/v Polyethylene glycol 4,000	Resolution 2.79 Å R-free 0.264
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 303–604	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.04 M HEPES sodium pH 7.5, 4% v/v 2-Propanol, 0.02 M Sodium citrate tribasic dihydrate, 2% w/v Polyethylene glycol 3,350, 8% w/v Polyethylene glycol 4,000	Resolution 2.79 Å R-free 0.264
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 303–604	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.04 M HEPES sodium pH 7.5, 4% v/v 2-Propanol, 0.02 M Sodium citrate tribasic dihydrate, 2% w/v Polyethylene glycol 3,350, 8% w/v Polyethylene glycol 4,000	Resolution 2.79 Å R-free 0.264

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 9WYS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VS7 Crystal structure of the ectodomain of OsCERK1 in complex with chitin hexamer Deposited 2021-10-26	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 27–237（211 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25M Magnesium chloride, 0.1 M TRIS, pH8.5, and 30% (w/v) PEG4000.	Resolution 2.02 Å R-free 0.235
9V70 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–604（329 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；5% v/v Polyethylene glycol 200, 0.05 M BIS-TRIS propane pH 9.0, 9% w/v Polyethylene glycol 8,000	Resolution 2.82 Å R-free 0.249
9V70 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 276–604（329 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；5% v/v Polyethylene glycol 200, 0.05 M BIS-TRIS propane pH 9.0, 9% w/v Polyethylene glycol 8,000	Resolution 2.82 Å R-free 0.249
9V70 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 276–604（329 aa） Chain B 276–604（329 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；5% v/v Polyethylene glycol 200, 0.05 M BIS-TRIS propane pH 9.0, 9% w/v Polyethylene glycol 8,000	Resolution 2.82 Å R-free 0.249
9V71 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 303–604（302 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Calcium acetate hydrate, 10% w/v Polyethylene glycol 3,350	Resolution 2.52 Å R-free 0.276
9V72 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 303–604（302 aa） Chain B 303–604（302 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.01 M Citric/0.025 M B-T propane ph7.1, 0.018 M Sodium malonate pH 5.0, 10.9% peg3350, 0.023 M glycyl-glycyl-glycine, 0.09 M NDSB-256	Resolution 2.75 Å R-free 0.273
9V73 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–604（329 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.06 M Potassium bromide, 0.02 M Ammonium acetate, 0.01 M HEPES pH 7.5, 12% w/v Polyethylene glycol monomethyl ether 2,000, 2.5% w/v Polyethylene glycol 3,350	Resolution 2.27 Å R-free 0.280
9V79 Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 303–604（302 aa）	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.08 M Calcium acetate hydrate, 0.2% v/v TacsimateTM pH 4.0, 0.01 M Sodium acetate trihydrate pH 4.6, 9.6% w/v Polyethylene glycol 3,350	Resolution 2.12 Å R-free 0.275
9V7E Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-05-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–604（329 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.06 M Potassium bromide, 0.02 M Ammonium acetate, 0.01 M Tris pH 8.5, 12% w/v Polyethylene glycol monomethyl ether 2,000, 2.5% w/v Polyethylene glycol 3,350	Resolution 1.97 Å R-free 0.272
9WYQ Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 303–604（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.08 M Magnesium acetate tetrahydrate, 0.01 M MES monohydrate pH 6.0, 2.2% Polyethylene glycol 400, 8% w/v Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.236
9WYR Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 303–604（302 aa） Chain B 303–604（302 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；(0.009 M Citric, 0.02M B-T propane) pH 7.1, 1.1% v/v TacsimateTM pH 7.0, 0.007 M HEPES pH 7.0, 0.009 M HEPES pH 7.5, 1.8% v/v Jeffamine M-600, 0.09 M Lithium chloride, 7.5% w/v Polyethylene glycol 3,350	Resolution 2.55 Å R-free 0.270
9WYR Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 303–604（302 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；(0.009 M Citric, 0.02M B-T propane) pH 7.1, 1.1% v/v TacsimateTM pH 7.0, 0.007 M HEPES pH 7.0, 0.009 M HEPES pH 7.5, 1.8% v/v Jeffamine M-600, 0.09 M Lithium chloride, 7.5% w/v Polyethylene glycol 3,350	Resolution 2.55 Å R-free 0.270
9WYR Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa Deposited 2025-09-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 303–604（302 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；(0.009 M Citric, 0.02M B-T propane) pH 7.1, 1.1% v/v TacsimateTM pH 7.0, 0.007 M HEPES pH 7.0, 0.009 M HEPES pH 7.5, 1.8% v/v Jeffamine M-600, 0.09 M Lithium chloride, 7.5% w/v Polyethylene glycol 3,350	Resolution 2.55 Å R-free 0.270

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

View Construct and Data Evidence

UniProt name	CERK1_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 303–604 Author chain B； PDBConstruct 1–302； UniProt 303–604

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	9wys
Deposition date deposition_date	2025-09-27
Structure title title	Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa
Keywords keywords	;OsCERK1-KD-ADP complex (ATP-treated), the kinase domain of OsCERK1 adopts the ADP-binding form after incubation with ATP, TRANSFERASE ;; TRANSFERASE
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	28.33 Å
Radius of gyration Rg (electron density) rg_electron	27.34 Å
Forward intensity I(0) i0	52566600.00
Molecular weight molecular_weight	57846.0 kDa
Excluded volume excluded_volume	73106 Å³
Envelope volume envelope_volume	94118 Å³
Hydration-shell volume shell_volume	28776 Å³
Envelope diameter envelope_diameter	85.7 Å
Shell Rg shell_rg	34.64 Å
Envelope Rg envelope_rg	26.78 Å
Shape Rg shape_rg	27.36 Å
Total Rg total_rg	28.13 Å
Total atoms total_atoms	4073
Residues n_residues	510
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	88.5 Å
Rg (real space) rg_real	28.24 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	5.2570e+07
I(0) uncertainty (real space) i0_real_error	7.8930e+05
Rg (reciprocal space) rg_reciprocal	28.27 Å
I(0) (reciprocal space) i0_reciprocal	52570000.0000
Solution quality estimate total_estimate	0.9063
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.136
Kurtosis Kurtosis kurtosis	-0.774
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26020000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.982

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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	Chitin elicitor receptor kinase 1
Molecular weight formula_weight	33478.2 kDa
EC 编号 ec_number	2.7.11.1
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	4104

GITVDKSVEFSYEELSNATQGFSIGNKIGQGGFGAVYYAELRGEKAAIKKMDMQATHEFLAELKVLTHVHHLNLVRLIGYCIESSLFLVYEFIENGNLSQHLRGMGYEPLSWAARIQIALDSARGLEYIHEHTVPVYIHRDIKSANILIDKNYRAKVADFGLTKLTEVGGTSMPTGTRVVGTFGYMPPEYARYGDVSPKVDVYAFGVVLYELISAKEAIVRSTESSSDSKGLVYLFEEALNSPDPKEGLRTLIDPKLGEDYPIDSILKLTQLAKVCTQEDPKLRPSMRSVVVALMTLSSTSE

来源 Source

来源生物 organism	Oryza sativa Japonica Group
通用名 common_name	Japanese rice
NCBI Class编号 ncbi_taxonomy_id	39947
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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8. Citations (1)

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Unit-cell length a length_a	109.910 Å
Unit-cell length b length_b	109.910 Å
Unit-cell length c length_c	120.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	36.913 Å
R factor r_factor	0.2315
R_work r_work	0.2280
R_free r_free	0.2638

fit	/app/data/saxs_computation/wy/9wys/9wys.fit
pddf	/app/data/pr_computation/wy/9wys/9wys.pr.out
profile	/app/data/saxs_computation/wy/9wys/9wys.dat

Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa

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

Chitin elicitor receptor kinase 1

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