SAXSdb — 8tlk

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

Cell division cycle-associated protein 7

Homo sapiens

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 232–371	Not recorded	DNA (32-MER) × 2 ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；0.2M MgCl2, 0.1 M Bis-Tris pH6.0, 25%PEG3350	Resolution 2.99 Å R-free 0.302
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 232–371	Not recorded	DNA (32-MER) × 2 ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；0.2M MgCl2, 0.1 M Bis-Tris pH6.0, 25%PEG3350	Resolution 2.99 Å R-free 0.302

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 8TLK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 264–371（108 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDCA7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–144； UniProt 232–371 Author chain B； PDBConstruct 5–144； UniProt 232–371

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	8tlk
Deposition date deposition_date	2023-07-26
Structure title title	CDCA7 (Human) Binds Non-B-form 32-mer DNA oligo Containing a 5mC
Keywords keywords	PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN, zinc fingers, chromatin architecture, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	32.89 Å
Radius of gyration Rg (electron density) rg_electron	31.23 Å
Forward intensity I(0) i0	57824800.00
Molecular weight molecular_weight	43698.0 kDa
Excluded volume excluded_volume	47773 Å³
Envelope volume envelope_volume	79722 Å³
Hydration-shell volume shell_volume	23557 Å³
Envelope diameter envelope_diameter	119.2 Å
Shell Rg shell_rg	33.83 Å
Envelope Rg envelope_rg	31.88 Å
Shape Rg shape_rg	31.13 Å
Total Rg total_rg	31.63 Å
Total atoms total_atoms	2947
Residues n_residues	268
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	112.0 Å
Rg (real space) rg_real	33.09 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	5.7820e+07
I(0) uncertainty (real space) i0_real_error	8.8510e+05
Rg (reciprocal space) rg_reciprocal	33.01 Å
I(0) (reciprocal space) i0_reciprocal	57820000.0000
Solution quality estimate total_estimate	0.8007
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.296
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2603000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.791; Smooth: 0.182

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Cell division cycle-associated protein 7
Molecular weight formula_weight	16418.7 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	3020

GPLGSVTLPHIIRPVEEITEEELENVCSNSREKIYNRSLGSTCHQCRQKTIDTKTNCRNPDCWGVRGQFCGPCLRNRYGEEVRDALLDPNWHCPPCRGICNCSFCRQRDGRCATGVLVYLAKYHGFGNVHAYLKSLKQEFEMQA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (32-MER)
Molecular weight formula_weight	9864.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X,C

CGACGCCCTGTCGCTGAGAAGCGTTTGCGTCG

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	6

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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8. Citations (1)

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Unit-cell length a length_a	173.479 Å
Unit-cell length b length_b	31.538 Å
Unit-cell length c length_c	94.566 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	43.060 Å
R factor r_factor	0.2454
R_work r_work	0.2426
R_free r_free	0.3018

fit	/app/data/saxs_computation/tl/8tlk/8tlk.fit
pddf	/app/data/pr_computation/tl/8tlk/8tlk.pr.out
profile	/app/data/saxs_computation/tl/8tlk/8tlk.dat

CDCA7 (Human) Binds Non-B-form 32-mer DNA oligo Containing a 5mC

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

Cell division cycle-associated protein 7

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)