SAXSdb — 2a1k

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

gp32 single stranded DNA binding protein

Enterobacteria phage RB69

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 21–253	Fragment：Core domain	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG200, MES, magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.259
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–253	Fragment：Core domain	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG200, MES, magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.259

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 2A1K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ATQ RB69 single-stranded DNA binding protein-DNA polymerase fusion Deposited 2005-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–253（233 aa） Fragment：RB69 single-stranded DNA binding protein	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 400, Tris-Cl, 6-aminocaproic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.20 Å R-free 0.345

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

View Construct and Data Evidence

UniProt name	Q7Y265_BPR69
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–233； UniProt 21–253 Author chain B； PDBConstruct 1–233； UniProt 21–253

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	2a1k
Deposition date deposition_date	2005-06-20
Structure title title	RB69 single-stranded DNA binding protein core domain
Keywords keywords	Zn2+ binding subdomain, 5-stranded beta-sheet, OB fold, single-stranded DNA binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	26.79 Å
Radius of gyration Rg (electron density) rg_electron	25.89 Å
Forward intensity I(0) i0	40050700.00
Molecular weight molecular_weight	48842.0 kDa
Excluded volume excluded_volume	61152 Å³
Envelope volume envelope_volume	80258 Å³
Hydration-shell volume shell_volume	26634 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	32.35 Å
Envelope Rg envelope_rg	25.60 Å
Shape Rg shape_rg	25.90 Å
Total Rg total_rg	26.67 Å
Total atoms total_atoms	3436
Residues n_residues	427
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	83.7 Å
Rg (real space) rg_real	26.76 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	4.0050e+07
I(0) uncertainty (real space) i0_real_error	6.0800e+05
Rg (reciprocal space) rg_reciprocal	26.77 Å
I(0) (reciprocal space) i0_reciprocal	40050000.0000
Solution quality estimate total_estimate	0.9061
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.280
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4573000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	gp32 single stranded DNA binding protein
Molecular weight formula_weight	26097.3 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	3872

KGFSSEDKGEWKLKLDASGNGQAVIRFLPAKTDDALPFAILVNHGFKKNGKWYIETCSSTHGDYDSCPVCQYISKNDLYNTNKTEYSQLKRKTSYWANILVVKDPQAPDNEGKVFKYRFGKKIWDKINAMIAVDTEMGETPVDVTCPWEGANFVLKVKQVSGFSNYDESKFLNQSAIPNIDDESFQKELFEQMVDLSEMTSKDKFKSFEELNTKFNQVLGTAALGGAAAAAAS

来源 Source

来源生物 organism	Enterobacteria phage RB69
NCBI Class编号 ncbi_taxonomy_id	12353
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2a1ka_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.7 — Phage ssDNA-binding proteins

Domain ID domain_id	d2a1kb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.7 — Phage ssDNA-binding proteins

CATH v4.4 (2 domains)

Domain ID domain_id	2a1kA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	198 — Replication Fork Single-Stranded DNA Binding Protein
Homologous superfamily homologous superfamily	10 — Replication Fork Single-Stranded Dna Binding Protein

Domain ID domain_id	2a1kB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	198 — Replication Fork Single-Stranded DNA Binding Protein
Homologous superfamily homologous superfamily	10 — Replication Fork Single-Stranded Dna Binding Protein

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8. Citations (1)

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Unit-cell length a length_a	67.700 Å
Unit-cell length b length_b	67.700 Å
Unit-cell length c length_c	123.750 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	47.870 Å
R factor r_factor	0.2430
R_work r_work	0.2360
R_free r_free	0.2590

fit	/app/data/saxs_computation/a1/2a1k/2a1k.fit
pddf	/app/data/pr_computation/a1/2a1k/2a1k.pr.out
profile	/app/data/saxs_computation/a1/2a1k/2a1k.dat

RB69 single-stranded DNA binding protein core domain

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

gp32 single stranded DNA binding protein

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