1a1k

RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE)

Method: X-RAY DIFFRACTION Dmax: 56.6 Å Quality: GOOD

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

RADR ZIF268 VARIANT

Mus musculus

UniProt P08046

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts Chain A; UniProt 308–396 Fragment:ZINC FINGER ;DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3') ; × 1 ;DNA (5'-D(*TP*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3') ; × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.2;25% PEG 1450, 25 MM MES PH 6.2 Resolution 1.90 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.

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGR1_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 2–90; UniProt 308–396

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

SAXS profile for 1a1k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a1k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a1k
Deposition date deposition_date1997-12-10
Structure title titleRADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE)
Keywords keywordsCOMPLEX (ZINC FINGER-DNA), ZINC FINGER, DNA-BINDING PROTEIN, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.11
Radius of gyration Rg (electron density) rg_electron15.92
Forward intensity I(0) i09287230.00
Molecular weight molecular_weight17020.0 kDa
Excluded volume excluded_volume18886 ų
Envelope volume envelope_volume23418 ų
Hydration-shell volume shell_volume12946 ų
Envelope diameter envelope_diameter60.0
Shell Rg shell_rg21.04
Envelope Rg envelope_rg16.39
Shape Rg shape_rg15.85
Total Rg total_rg16.77
Total atoms total_atoms1156
Residues n_residues107
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax56.6
Rg (real space) rg_real16.10
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real9.2870e+06
I(0) uncertainty (real space) i0_real_error1.1300e+05
Rg (reciprocal space) rg_reciprocal16.10
I(0) (reciprocal space) i0_reciprocal9287000.0000
Solution quality estimate total_estimate0.7714
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.1
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.022
Angular range angular_range— – 0.4950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1211000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.693; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1a1ka1
Class classg — Small proteins
Fold Fold foldg.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamilyg.37.1 — beta-beta-alpha zinc fingers
Family Family familyg.37.1.1 — Classic zinc finger, C2H2
Domain ID domain_idd1a1ka2
Class classg — Small proteins
Fold Fold foldg.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamilyg.37.1 — beta-beta-alpha zinc fingers
Family Family familyg.37.1.1 — Classic zinc finger, C2H2
Domain ID domain_idd1a1ka3
Class classg — Small proteins
Fold Fold foldg.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamilyg.37.1 — beta-beta-alpha zinc fingers
Family Family familyg.37.1.1 — Classic zinc finger, C2H2

CATH v4.4 (3 domains)

Domain ID domain_id1a1kA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily60 — Classic Zinc Finger
Domain ID domain_id1a1kA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily60 — Classic Zinc Finger
Domain ID domain_id1a1kA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily60 — Classic Zinc Finger

8. Citations (4)

9. Files and Curves (10)