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1b43

FEN-1 FROM P. FURIOSUS

Method: X-RAY DIFFRACTION Dmax: 89.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (FEN-1)

Pyrococcus furiosus

UniProt O93634

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–340 Chain B； UniProt 1–340 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；60 % AMMONIUM SULFATE 100 MM IMIDAZOLE MALATE 50 MM MGCL2, pH 6.5 Resolution 2.00 Å R-free 0.279

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 1B43 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VBH Human XPG endonuclease catalytic domain Deposited 2019-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 89–128（40 aa）
Not recorded SO4 SULFATE ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2
Resolution 2.00 Å R-free 0.244
6VBH Human XPG endonuclease catalytic domain Deposited 2019-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 89–128（40 aa）
Not recorded SO4 SULFATE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2
Resolution 2.00 Å R-free 0.244

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

View Construct and Data Evidence
UniProt name FEN_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–340； UniProt 1–340 Author chain B； PDBConstruct 1–340； UniProt 1–340

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 1b43

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b43
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b43
Deposition date deposition_date1999-01-05
Structure title titleFEN-1 FROM P. FURIOSUS
Keywords keywordsNUCLEASE, DNA REPAIR, DNA REPLICATION, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.19 Å
Radius of gyration Rg (electron density) rg_electron27.18 Å
Forward intensity I(0) i091402500.00
Molecular weight molecular_weight77217.0 kDa
Excluded volume excluded_volume98085 ų
Envelope volume envelope_volume125870 ų
Hydration-shell volume shell_volume37468 ų
Envelope diameter envelope_diameter97.1 Å
Shell Rg shell_rg35.35 Å
Envelope Rg envelope_rg27.32 Å
Shape Rg shape_rg27.15 Å
Total Rg total_rg28.23 Å
Total atoms total_atoms5444
Residues n_residues678
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.6 Å
Rg (real space) rg_real28.03 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real9.1400e+07
I(0) uncertainty (real space) i0_real_error1.2050e+06
Rg (reciprocal space) rg_reciprocal28.08 Å
I(0) (reciprocal space) i0_reciprocal91410000.0000
Solution quality estimate total_estimate0.7235
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.6 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20000000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.996; Smooth: 0.981
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1b43a1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family familya.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_idd1b43a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.120 — PIN domain-like
Superfamily Superfamily superfamilyc.120.1 — PIN domain-like
Family Family familyc.120.1.2 — 5' to 3' exonuclease catalytic domain
Domain ID domain_idd1b43b1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family familya.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_idd1b43b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.120 — PIN domain-like
Superfamily Superfamily superfamilyc.120.1 — PIN domain-like
Family Family familyc.120.1.2 — 5' to 3' exonuclease catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id1b43A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1010 — 5'-nuclease
Domain ID domain_id1b43A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1b43B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1010 — 5'-nuclease
Domain ID domain_id1b43B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)