SAXSdb — 5mec

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

Cell division cycle protein CDT1

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 272–438	Fragment：UNP residues 272-438	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BTP pH 5.5, 2M ammonium sulphate	Resolution 2.13 Å R-free 0.244

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 5MEC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5ME9 Crystal structure of yeast Cdt1 (N terminal and middle domain), form 1. Deposited 2016-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–438（437 aa） Fragment：UNP residues 2-438	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% Glycerol, 20% PEG 4000, 20% 2-Propanol, 0.1M Tris-HCl pH8.5	Resolution 2.70 Å R-free 0.231
5ME9 Crystal structure of yeast Cdt1 (N terminal and middle domain), form 1. Deposited 2016-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–438（437 aa） Fragment：UNP residues 2-438	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% Glycerol, 20% PEG 4000, 20% 2-Propanol, 0.1M Tris-HCl pH8.5	Resolution 2.70 Å R-free 0.231
5ME9 Crystal structure of yeast Cdt1 (N terminal and middle domain), form 1. Deposited 2016-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–438（437 aa） Fragment：UNP residues 2-438	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% Glycerol, 20% PEG 4000, 20% 2-Propanol, 0.1M Tris-HCl pH8.5	Resolution 2.70 Å R-free 0.231
5MEA Crystal structure of yeast Cdt1 (N terminal and middle domain), form 2. Deposited 2016-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–438（438 aa）	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；10.5% PEG 8K, 18% glycerol, 0.5M lithium sulphate	Resolution 2.15 Å R-free 0.249
5MEB Crystal structure of yeast Cdt1 C-terminal domain Deposited 2016-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 495–604（110 aa） Fragment：UNP residues 495-604	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% glycerol, 0.1M MES pH 6.5, 1.8M ammonium sulphate	Resolution 1.80 Å R-free 0.210
5MEB Crystal structure of yeast Cdt1 C-terminal domain Deposited 2016-11-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 495–604（110 aa） Fragment：UNP residues 495-604	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% glycerol, 0.1M MES pH 6.5, 1.8M ammonium sulphate	Resolution 1.80 Å R-free 0.210
5V8F Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1 Deposited 2017-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain 8 1–604（604 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
5XF8 Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state Deposited 2017-04-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–604（604 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6WGG Atomic model of pre-insertion mutant OCCM-DNA complex(ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain 8 1–604（604 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.10 Å
6WGI Atomic model of the mutant OCCM (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) loaded on DNA at 10.5 A resolution Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain L 1–604（604 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.00 Å
9GJP OCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm5: Conformer 2 Deposited 2024-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain 8 1–604（604 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ZN ZINC ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9GJW OCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm2 Deposited 2024-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain 8 1–604（604 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9GM5 OCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm5: Conformer 1 Deposited 2024-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain 8 1–604（604 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 ZN ZINC ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	CDT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–169； UniProt 272–438

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	5mec
Deposition date deposition_date	2016-11-14
Structure title title	Crystal structure of yeast Cdt1 middle domain (residues 294-433)
Keywords keywords	Cdt1, MCM, winged helix, yeast, DNA replication, cell cycle; CELL CYCLE
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	17.69 Å
Radius of gyration Rg (electron density) rg_electron	16.58 Å
Forward intensity I(0) i0	4166630.00
Molecular weight molecular_weight	15043.0 kDa
Excluded volume excluded_volume	19138 Å³
Envelope volume envelope_volume	23024 Å³
Hydration-shell volume shell_volume	12533 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	21.71 Å
Envelope Rg envelope_rg	17.37 Å
Shape Rg shape_rg	16.59 Å
Total Rg total_rg	17.62 Å
Total atoms total_atoms	1056
Residues n_residues	131
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	68.1 Å
Rg (real space) rg_real	17.81 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.1670e+06
I(0) uncertainty (real space) i0_real_error	6.0390e+04
Rg (reciprocal space) rg_reciprocal	17.80 Å
I(0) (reciprocal space) i0_reciprocal	4167000.0000
Solution quality estimate total_estimate	0.7760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.587
Kurtosis Kurtosis kurtosis	0.230
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	905300.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.492; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.613; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	45.130 Å
Unit-cell length b length_b	46.330 Å
Unit-cell length c length_c	75.360 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	39.468 Å
R factor r_factor	0.1989
R_work r_work	0.1965
R_free r_free	0.2440

Description description	Cell division cycle protein CDT1
Molecular weight formula_weight	19280.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1148

Crystal structure of yeast Cdt1 middle domain (residues 294-433)

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

Cell division cycle protein CDT1

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

fit	/app/data/saxs_computation/me/5mec/5mec.fit
pddf	/app/data/pr_computation/me/5mec/5mec.pr.out
profile	/app/data/saxs_computation/me/5mec/5mec.dat