SAXSdb — 4xhl

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

Casein kinase I homolog HRR25

Saccharomyces cerevisiae

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 1–394	Fragment：UNP residues 1-394 Mutation：K38R	CKI N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE × 1 SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 11；293 K；0.1 M CAPS pH 11, 0.2 M lithium sulfate, and 1.5-1.6 M ammonium sulfate	Resolution 3.01 Å R-free 0.285

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 4XHL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CYZ Structure of S. cerevisiae Hrr25:Mam1 complex, form 1 Deposited 2015-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa）	Mutation：K38R, N-terminal Ala from tag Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；0.1M CHES pH8.9, 5% Tacsimate, 25 mM YCl3, 19% PEG3350	Resolution 1.84 Å R-free 0.192
5CZO Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 Deposited 2015-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa）	Mutation：K38R Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Imidazole pH 8.0, 14% PEG3350, 6% Glycerol	Resolution 2.89 Å R-free 0.253
5CZO Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 Deposited 2015-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–394（394 aa）	Mutation：K38R Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Imidazole pH 8.0, 14% PEG3350, 6% Glycerol	Resolution 2.89 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	HRR25_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394

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	4xhl
Deposition date deposition_date	2015-01-05
Structure title title	Structure of S. cerevisiae Hrr25 1-394 (K38R mutant)
Keywords keywords	casein kinase, monopolin, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	22.10 Å
Radius of gyration Rg (electron density) rg_electron	20.97 Å
Forward intensity I(0) i0	27560100.00
Molecular weight molecular_weight	39940.0 kDa
Excluded volume excluded_volume	49903 Å³
Envelope volume envelope_volume	61052 Å³
Hydration-shell volume shell_volume	23892 Å³
Envelope diameter envelope_diameter	70.6 Å
Shell Rg shell_rg	28.18 Å
Envelope Rg envelope_rg	21.35 Å
Shape Rg shape_rg	20.94 Å
Total Rg total_rg	21.99 Å
Total atoms total_atoms	2804
Residues n_residues	330
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	68.5 Å
Rg (real space) rg_real	21.97 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.7560e+07
I(0) uncertainty (real space) i0_real_error	3.1850e+05
Rg (reciprocal space) rg_reciprocal	21.99 Å
I(0) (reciprocal space) i0_reciprocal	27560000.0000
Solution quality estimate total_estimate	0.8905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.170
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6003000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.789

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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	Casein kinase I homolog HRR25
Molecular weight formula_weight	45934.6 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	K38R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2811

MDLRVGRKFRIGRKIGSGSFGDIYHGTNLISGEEVAIRLESIRSRHPQLDYESRVYRYLSGGVGIPFIRWFGREGEYNAMVIDLLGPSLEDLFNYCHRRFSFKTVIMLALQMFCRIQYIHGRSFIHRDIKPDNFLMGVGRRGSTVHVIDFGLSKKYRDFNTHRHIPYRENKSLTGTARYASVNTHLGIEQSRRDDLESLGYVLIYFCKGSLPWQGLKATTKKQKYDRIMEKKLNVSVETLCSGLPLEFQEYMAYCKNLKFDEKPDYLFLARLFKDLSIKLEYHNDHLFDWTMLRYTKAMVEKQRDLLIEKGDLNANSNAASASNSTDNKSETFNKIKLLAMKKFPTHFHYYKNEDKHNPSPEEIKQQTILNNNAASSLPEELLNALDKGMENLR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE
Molecular weight formula_weight	285.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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8. Citations (1)

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Unit-cell length a length_a	137.497 Å
Unit-cell length b length_b	137.497 Å
Unit-cell length c length_c	94.639 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 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	119.080 Å
R factor r_factor	0.2679
R_work r_work	0.2670
R_free r_free	0.2847

fit	/app/data/saxs_computation/xh/4xhl/4xhl.fit
pddf	/app/data/pr_computation/xh/4xhl/4xhl.pr.out
profile	/app/data/saxs_computation/xh/4xhl/4xhl.dat

Structure of S. cerevisiae Hrr25 1-394 (K38R mutant)

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

Casein kinase I homolog HRR25

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