1d8b

NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE

Method: SOLUTION NMR D_max: 37.1 Å Quality: GOOD

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

SGS1 RECQ HELICASE

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 1271–1351	Fragment：HRDC DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；295 K；Ionic strength (raw mmCIF value) 20 mM SODIUM PHOSPHATE；Pressure 1 NMR sample composition：13C-15N-LABELED SAMPLE \| 20 mM sodium phosphate buffer NMR sample composition：15N-LABELED SAMPLE \| 20 mM sodium phosphate buffer	Resolution not provided

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	SGS1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–81； UniProt 1271–1351

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d8b
Deposition date deposition_date	1999-10-21
Structure title title	NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE
Keywords keywords	FIVE HELICES, THREE-HELICAL BUNDLE FLANKED BY TWO HELICES, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.79 Å
Radius of gyration Rg (electron density) rg_electron	12.41 Å
Forward intensity I(0) i0	273884000.00
Molecular weight molecular_weight	140660.0 kDa
Excluded volume excluded_volume	177020 Å³
Envelope volume envelope_volume	20077 Å³
Hydration-shell volume shell_volume	12172 Å³
Envelope diameter envelope_diameter	47.4 Å
Shell Rg shell_rg	19.80 Å
Envelope Rg envelope_rg	14.54 Å
Shape Rg shape_rg	12.38 Å
Total Rg total_rg	12.68 Å
Total atoms total_atoms	20040
Residues n_residues	1215
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	37.1 Å
Rg (real space) rg_real	12.74 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.7390e+08
I(0) uncertainty (real space) i0_real_error	2.8170e+06
Rg (reciprocal space) rg_reciprocal	12.74 Å
I(0) (reciprocal space) i0_reciprocal	273900000.0000
Solution quality estimate total_estimate	0.8291
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.6 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	129600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.011

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d8ba_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.8 — HRDC-like
Family Family family	a.60.8.1 — HRDC domain from helicases

CATH v4.4 (1 domains)

Domain ID domain_id	1d8bA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	SGS1 RECQ HELICASE
Molecular weight formula_weight	9386.0 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	20040

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

NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE

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

SGS1 RECQ HELICASE

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/d8/1d8b/1d8b.fit
pddf	/app/data/pr_computation/d8/1d8b/1d8b.pr.out
profile	/app/data/saxs_computation/d8/1d8b/1d8b.dat