SAXSdb — 1c1k

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

BPT4 GENE 59 HELICASE ASSEMBLY PROTEIN

Enterobacteria phage T4

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 1–217	Not recorded	IR IRIDIUM ION × 2 CL CHLORIDE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 MM NA CACODYLATE, PH 6.5 200 MM NH4 ACETATE, 50 MM (NH4)2SO4, 10 - 14% PEG 3350 GRADIENT, 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.253

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	VG59_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1–217

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	1c1k
Deposition date deposition_date	1999-07-22
Structure title title	BACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN
Keywords keywords	HELICASE ASSEMBLY, DNA REPLICATION, DNA RECOMBINATION, FORKED DNA, 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	20.46 Å
Radius of gyration Rg (electron density) rg_electron	19.21 Å
Forward intensity I(0) i0	12317300.00
Molecular weight molecular_weight	26818.0 kDa
Excluded volume excluded_volume	33661 Å³
Envelope volume envelope_volume	38855 Å³
Hydration-shell volume shell_volume	17574 Å³
Envelope diameter envelope_diameter	67.9 Å
Shell Rg shell_rg	24.59 Å
Envelope Rg envelope_rg	19.48 Å
Shape Rg shape_rg	19.03 Å
Total Rg total_rg	20.56 Å
Total atoms total_atoms	1852
Residues n_residues	217
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	68.0 Å
Rg (real space) rg_real	20.48 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.2320e+07
I(0) uncertainty (real space) i0_real_error	1.6040e+05
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	12320000.0000
Solution quality estimate total_estimate	0.8757
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.154
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1428000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BPT4 GENE 59 HELICASE ASSEMBLY PROTEIN
Molecular weight formula_weight	26036.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2150

MIKLRMPAGGERYIDGKSVYKLYLMIKQHMNGKYDVIKYNWCMRVSDAAYQKRRDKYFFQKLSEKYKLKELALIFISNLVANQDAWIGDISDADALVFYREYIGRLKQIKFKFEEDIRNIYYFSKKVEVSAFKEIFEYNPKVQSSYIFKLLQSNIISFETFILLDSFLNIIDKHDEQTDNLVWNNYSIKLKAYRKILNIDSQKAKNVFIETVKSCKY

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRIDIUM ION
Molecular weight formula_weight	192.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c1ka_
Class class	a — All alpha proteins
Fold Fold fold	a.120 — gene 59 helicase assembly protein
Superfamily Superfamily superfamily	a.120.1 — gene 59 helicase assembly protein
Family Family family	a.120.1.1 — gene 59 helicase assembly protein

CATH v4.4 (2 domains)

Domain ID domain_id	1c1kA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1c1kA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	50 — Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	31.865 Å
Unit-cell length b length_b	65.882 Å
Unit-cell length c length_c	108.166 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	1.450 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.2050
R_work r_work	0.2000
R_free r_free	0.2530

fit	/app/data/saxs_computation/c1/1c1k/1c1k.fit
pddf	/app/data/pr_computation/c1/1c1k/1c1k.pr.out
profile	/app/data/saxs_computation/c1/1c1k/1c1k.dat

BACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN

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

BPT4 GENE 59 HELICASE ASSEMBLY 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