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1d2m

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

Method: X-RAY DIFFRACTION Dmax: 88.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EXCINUCLEASE ABC SUBUNIT B

Thermus thermophilus

UniProt Q56243

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 1–665 Not recorded BOG octyl beta-D-glucopyranoside × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；lithium sulfate, B-octylgulucoside, glycerol, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.90 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.

Other PDB Difference from Current Entry 1D2M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C4O CRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB FROM THERMUS THERMOPHILUS Deposited 1999-09-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–665（664 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；4 MICROLITERS PROTEIN (14 MG/ML IN 50 MM TRIS/CL, 1 MM EDTA, 5 MM DTT, 10% (V/ V) GLYCEROL, PH 7.5) WERE MIXED WITH 4 MICROLITERS RESERVOIR SOLUTION (1.7-1.9 M LITHIUM SULFATE, 0.1 M MES, 0.5% (W/V) BETA-OCTYLGLUCOSIDE, PH 6.0) AND EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION AT 293 K., VAPOR DIFFUSION, HANGING DROP
Resolution 1.50 Å R-free 0.266
7EGT The crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB Deposited 2021-03-26 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 A 1–408（408 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500
Resolution 2.58 Å R-free 0.249
7EGT The crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB Deposited 2021-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–408（408 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500
Resolution 2.58 Å R-free 0.249

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UVRB_THET8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–665； UniProt 1–665

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 1d2m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d2m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d2m
Deposition date deposition_date1999-09-25
Structure title titleUVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME
Keywords keywordsMULTIDOMAIN PROTEIN, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, HYDROLASE; HYDROLASE
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_guinier28.20 Å
Radius of gyration Rg (electron density) rg_electron27.40 Å
Forward intensity I(0) i064281600.00
Molecular weight molecular_weight64084.0 kDa
Excluded volume excluded_volume80889 ų
Envelope volume envelope_volume100100 ų
Hydration-shell volume shell_volume30822 ų
Envelope diameter envelope_diameter94.2 Å
Shell Rg shell_rg34.51 Å
Envelope Rg envelope_rg27.43 Å
Shape Rg shape_rg27.37 Å
Total Rg total_rg28.25 Å
Total atoms total_atoms4524
Residues n_residues552
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 dmax88.8 Å
Rg (real space) rg_real28.18 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real6.4280e+07
I(0) uncertainty (real space) i0_real_error9.6430e+05
Rg (reciprocal space) rg_reciprocal28.19 Å
I(0) (reciprocal space) i0_reciprocal64280000.0000
Solution quality estimate total_estimate0.9064
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.2 Å
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.558
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16450000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d2ma1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd1d2ma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain

CATH v4.4 (4 domains)

Domain ID domain_id1d2mA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1d2mA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2060 — Penicillin-binding protein 1b fold
Homologous superfamily homologous superfamily10 — Penicillin-binding protein 1b domain
Domain ID domain_id1d2mA03
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily240 —
Domain ID domain_id1d2mA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (2)

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9. Files and Curves (10)