SAXSdb — 5ktb

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

Monopolin complex subunit CSM1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–190 Chain B； UniProt 1–190	Not recorded	Monopolin complex subunit MAM1 × 1 （P40065）	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

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 5KTB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3N4R Structure of Csm1 C-terminal domain, R3 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain B 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, temperature 293K	Resolution 2.60 Å R-free 0.243
3N4R Structure of Csm1 C-terminal domain, R3 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain D 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, temperature 293K	Resolution 2.60 Å R-free 0.243
3N4S Structure of Csm1 C-terminal domain, P21212 form Deposited 2010-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain B 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Not recorded	1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.234
3N4S Structure of Csm1 C-terminal domain, P21212 form Deposited 2010-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain D 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Not recorded	1PE PENTAETHYLENE GLYCOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.234
3N4X Structure of Csm1 full-length Deposited 2010-05-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Chain B 1–190（190 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；150 mM lithium chloride, 12% PEG 2000, 4% 1,4-butanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.41 Å R-free 0.282
3N4X Structure of Csm1 full-length Deposited 2010-05-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Chain D 1–190（190 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；150 mM lithium chloride, 12% PEG 2000, 4% 1,4-butanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.41 Å R-free 0.282
3N7N Structure of Csm1/Lrs4 complex Deposited 2010-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–190（190 aa） Chain B 1–190（190 aa） Chain C 1–190（190 aa） Chain D 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 120 mM MgCl2, 16% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.90 Å R-free 0.355
5V1A Structure of S. cerevisiae Ulp2:Csm1 complex Deposited 2017-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–190（122 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 M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol	Resolution 2.14 Å R-free 0.278
5V3N Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex Deposited 2017-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–181（113 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium Acetate, 0.1 M HEPES pH 7.5 and 25% PEG 3350 and 25% Glycerol	Resolution 1.30 Å R-free 0.217
6DEI Structure of Dse3-Csm1 complex Deposited 2018-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–181（113 aa） Chain B 69–181（113 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M NaOAc, 0.1M HEPES pH 7.5, 22% PEG 4000	Resolution 1.70 Å R-free 0.221

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSM1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 1–190 Author chain B； PDBConstruct 1–190； UniProt 1–190

Monopolin complex subunit MAM1

Saccharomyces cerevisiae

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 221–290	Not recorded	Monopolin complex subunit CSM1 × 2 （P25651）	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

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 5KTB	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 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 8.9；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 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 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 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

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 1–70； UniProt 221–290

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	5ktb
Deposition date deposition_date	2016-07-11
Structure title title	Structure of a complex between S. cerevisiae Csm1 and Mam1
Keywords keywords	monopolin, REPLICATION; REPLICATION
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	31.99 Å
Radius of gyration Rg (electron density) rg_electron	33.44 Å
Forward intensity I(0) i0	25381300.00
Molecular weight molecular_weight	40132.0 kDa
Excluded volume excluded_volume	50648 Å³
Envelope volume envelope_volume	69121 Å³
Hydration-shell volume shell_volume	20749 Å³
Envelope diameter envelope_diameter	128.3 Å
Shell Rg shell_rg	32.76 Å
Envelope Rg envelope_rg	35.07 Å
Shape Rg shape_rg	33.39 Å
Total Rg total_rg	33.53 Å
Total atoms total_atoms	2834
Residues n_residues	351
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	127.2 Å
Rg (real space) rg_real	33.10 Å
Rg uncertainty (real space) rg_real_error	1.83 Å
I(0) (real space) i0_real	2.5380e+07
I(0) uncertainty (real space) i0_real_error	4.7060e+05
Rg (reciprocal space) rg_reciprocal	32.63 Å
I(0) (reciprocal space) i0_reciprocal	25370000.0000
Solution quality estimate total_estimate	0.6543
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.891
Kurtosis Kurtosis kurtosis	0.143
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2867000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.185; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.085; Smooth: 0.861

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Monopolin complex subunit CSM1
Molecular weight formula_weight	21776.4 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	2834

MDPLTVYKNSVKQQIDSADLLVANLVNENFVLSEKLDTKATEIKQLQKQIDSLNAQVKELKTQTSQQAENSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNKKREKKDETE

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 polymer

Description description	Monopolin complex subunit MAM1
Molecular weight formula_weight	8042.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QKKRFLPQSVLIKREDEIAFDDFHLDARKVLNDLSATSENPFSSSPNTKKIKSKGKTLEVVPKKKNKKII

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

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5ktbA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	5ktbA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	5ktbB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	5ktbB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Unit-cell length a length_a	101.851 Å
Unit-cell length b length_b	101.851 Å
Unit-cell length c length_c	225.077 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	3.050 Å
Low-resolution limit resolution_low	24.920 Å
R factor r_factor	0.2146
R_work r_work	0.2132
R_free r_free	0.2406

fit	/app/data/saxs_computation/kt/5ktb/5ktb.fit
pddf	/app/data/pr_computation/kt/5ktb/5ktb.pr.out
profile	/app/data/saxs_computation/kt/5ktb/5ktb.dat

Structure of a complex between S. cerevisiae Csm1 and Mam1

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

Monopolin complex subunit CSM1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)