SAXSdb — 5cyz

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

Casein kinase I homolog HRR25

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 A； UniProt 1–394	Mutation：K38R, N-terminal Ala from tag Non-standard monomer：Yes (specific site not provided by mmCIF)	Monopolin complex subunit MAM1 × 1 （P40065） 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

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 5CYZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4XHL Structure of S. cerevisiae Hrr25 1-394 (K38R mutant) Deposited 2015-01-05	Different construct Different mutation/modification 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 1–394（394 aa） 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
5CZO Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 Deposited 2015-07-31	Different mutation/modification 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 mutation/modification 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 2–395； UniProt 1–394

Monopolin complex subunit MAM1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P40065

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 C； UniProt 87–191	Non-standard monomer：Yes (specific site not provided by mmCIF)	Casein kinase I homolog HRR25 × 1 （P29295） 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

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 5CYZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CZO Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 Deposited 2015-07-31	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 87–191（105 aa）	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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 87–191（105 aa）	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
5KTB Structure of a complex between S. cerevisiae Csm1 and Mam1 Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 221–290（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, pH 7.5, 100 mM magnesium chloride, 6% PEG4000	Resolution 3.05 Å R-free 0.241

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

View Construct and Data Evidence

UniProt name	MAM1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–105； UniProt 87–191

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	5cyz
Deposition date deposition_date	2015-07-31
Structure title title	Structure of S. cerevisiae Hrr25:Mam1 complex, form 1
Keywords keywords	casein kinase, monopolin, 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	24.46 Å
Radius of gyration Rg (electron density) rg_electron	23.23 Å
Forward intensity I(0) i0	50201200.00
Molecular weight molecular_weight	56172.0 kDa
Excluded volume excluded_volume	70834 Å³
Envelope volume envelope_volume	84439 Å³
Hydration-shell volume shell_volume	29332 Å³
Envelope diameter envelope_diameter	80.1 Å
Shell Rg shell_rg	31.17 Å
Envelope Rg envelope_rg	23.51 Å
Shape Rg shape_rg	23.20 Å
Total Rg total_rg	24.27 Å
Total atoms total_atoms	3955
Residues n_residues	452
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	75.8 Å
Rg (real space) rg_real	24.31 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	5.0200e+07
I(0) uncertainty (real space) i0_real_error	7.0070e+05
Rg (reciprocal space) rg_reciprocal	24.35 Å
I(0) (reciprocal space) i0_reciprocal	50200000.0000
Solution quality estimate total_estimate	0.8294
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.146
Kurtosis Kurtosis kurtosis	-0.549
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14050000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 0.998; Sysdev: 1.000; 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 (4)

Entity 1 Entity 1 polymer

Description description	Casein kinase I homolog HRR25
Molecular weight formula_weight	46438.4 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	K38R, N-terminal Ala from tag
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	4308

AMDLRVGRKFRIGRKIGSGSFGDIYHGTNLISGEEVAIRLESIRSRHPQLDYESRVYRYLSGGVGIPFIRWFGREGEYNAMVIDLLGPSLEDLFNYCHRRFSFKTVIMLALQMFCRIQYIHGRSFIHRDIKPDNFLMGVGRRGSTVHVIDFGLSKKYRDFNTHRHIPYRENKSLTGTARYASVNTHLGIEQSRRDDLESLGYVLIYFCKGSLPWQGLKATTKKQKYDRIMEKKLNVSVETLCSGLPLEFQEYMAYCKNLKFDEKPDYLFLARLFKDLSIKLEYHNDHLFDWTMLRYTKAMVEKQRDLLIEKGDLNANSNAASASNSTDNKSETFNKIKLLAMKKFPTHFHYYKNEDKHNPSPEEIKQQTILNNNAASSLPEELLNALDKGMENLR

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Monopolin complex subunit MAM1
Molecular weight formula_weight	12903.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EATECLTRSNLKKLQEKIFDRELNDIACDHCLCSTENRRDIKYSRLWFLFELEMSENWNENLRLSCYNKYVYSAIDESWKMENILLKEQEKHYEYFPIGQLLIPN

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

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8. Citations (1)

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Unit-cell length a length_a	54.190 Å
Unit-cell length b length_b	83.986 Å
Unit-cell length c length_c	67.424 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.53 °
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	1.841 Å
Low-resolution limit resolution_low	48.200 Å
R factor r_factor	0.1647
R_work r_work	0.1632
R_free r_free	0.1921

fit	/app/data/saxs_computation/cy/5cyz/5cyz.fit
pddf	/app/data/pr_computation/cy/5cyz/5cyz.pr.out
profile	/app/data/saxs_computation/cy/5cyz/5cyz.dat

Structure of S. cerevisiae Hrr25:Mam1 complex, form 1

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

Monopolin complex subunit MAM1

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 (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 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)