SAXSdb — 4dov

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

Origin recognition complex subunit 1

Mus musculus

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 9–170	Fragment：BAH domain (UNP residues 9-170) Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M 3-(1-pyridino)-1-propane sulfonate, 0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.70 Å R-free 0.243
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 9–170	Fragment：BAH domain (UNP residues 9-170) Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M 3-(1-pyridino)-1-propane sulfonate, 0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.70 Å R-free 0.243

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 4DOV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–170（162 aa） Fragment：BAH domain (UNP residues 9-170)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 9–170（162 aa） Fragment：BAH domain (UNP residues 9-170)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257

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

View Construct and Data Evidence

UniProt name	ORC1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–163； UniProt 9–170 Author chain C； PDBConstruct 2–163； UniProt 9–170

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	4dov
Deposition date deposition_date	2012-02-10
Structure title title	Structure of free mouse ORC1 BAH domain
Keywords keywords	DNA replication, 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	24.24 Å
Radius of gyration Rg (electron density) rg_electron	23.23 Å
Forward intensity I(0) i0	19545300.00
Molecular weight molecular_weight	35042.0 kDa
Excluded volume excluded_volume	44481 Å³
Envelope volume envelope_volume	56251 Å³
Hydration-shell volume shell_volume	20966 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	29.36 Å
Envelope Rg envelope_rg	23.09 Å
Shape Rg shape_rg	23.24 Å
Total Rg total_rg	24.06 Å
Total atoms total_atoms	2467
Residues n_residues	307
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	79.8 Å
Rg (real space) rg_real	24.21 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.9550e+07
I(0) uncertainty (real space) i0_real_error	2.5230e+05
Rg (reciprocal space) rg_reciprocal	24.22 Å
I(0) (reciprocal space) i0_reciprocal	19550000.0000
Solution quality estimate total_estimate	0.8955
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3766000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.941

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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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4dovA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	490 — Bromo adjacent homology (BAH) domain

Domain ID domain_id	4dovC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	490 — Bromo adjacent homology (BAH) domain

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8. Citations (1)

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Unit-cell length a length_a	49.922 Å
Unit-cell length b length_b	53.916 Å
Unit-cell length c length_c	71.971 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.696 Å
Low-resolution limit resolution_low	22.414 Å
R factor r_factor	0.2159
R_work r_work	0.2146
R_free r_free	0.2431

Description description	Origin recognition complex subunit 1
Molecular weight formula_weight	19039.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2707

Structure of free mouse ORC1 BAH domain

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

Origin recognition complex subunit 1

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

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
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	240

fit	/app/data/saxs_computation/do/4dov/4dov.fit
pddf	/app/data/pr_computation/do/4dov/4dov.pr.out
profile	/app/data/saxs_computation/do/4dov/4dov.dat