← Back to search
6m9k

Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain

Method: X-RAY DIFFRACTION Dmax: 100.7 Å Quality: EXCELLENT
▼

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

Exonuclease

Escherichia phage lambda

UniProt P03697

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–226 Chain B； UniProt 1–226 Chain C； UniProt 1–226 Not recorded Recombination protein bet × 3 （P03698） SO4 SULFATE ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；PEG3350, LISO4, BIS-TRIS Resolution 2.30 Å R-free 0.254

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 6M9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AVQ TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS Deposited 1997-09-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Chain C 1–226（226 aa）
Mutation：20 AMINO ACID N-TERMINAL HIS-TAG Mutation：20 AMINO ACID N-TERMINAL HIS-TAG Mutation：20 AMINO ACID N-TERMINAL HIS-TAG PO4 PHOSPHATE ION × 3 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.7；277 K；PROTEIN WAS CRYSTALLIZED FROM 1.2 M NH2SO4, 0.2 M NACL 0.1 M NAACETATE PH 4.7, AT 4 DEGREES CELSIUS., temperature 277K
Resolution 2.40 Å
3SLP Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex Deposited 2011-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Chain C 1–226（226 aa）
Not recorded CA CALCIUM ION × 3 PO4 PHOSPHATE ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；22% PEG3350, 0.3 M sodium acetate, 0.1 M Tris, 5 mM calcium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.30 Å R-free 0.281
3SM4 Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium Deposited 2011-06-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Chain C 1–226（226 aa）
Mutation：K131A Mutation：K131A Mutation：K131A PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；19% PEG3350, 0.2 M sodium bromide, 5 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.88 Å R-free 0.186
4WUZ Crystal structure of lambda exonuclease in complex with DNA and Ca2+ Deposited 2014-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Chain C 1–226（226 aa）
Not recorded CA CALCIUM ION × 3 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；23.4% PEG 3350, 0.3M sodium acetate, 0.1 M Tris
Resolution 2.38 Å R-free 0.319

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EXO_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–226； UniProt 1–226 Author chain B； PDBConstruct 1–226； UniProt 1–226 Author chain C； PDBConstruct 1–226； UniProt 1–226

Recombination protein bet

Escherichia phage lambda

UniProt P03698

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain D； UniProt 194–260 Chain E； UniProt 194–260 Chain F； UniProt 194–260 Not recorded Exonuclease × 3 （P03697） SO4 SULFATE ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；PEG3350, LISO4, BIS-TRIS Resolution 2.30 Å R-free 0.254

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 6M9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UJL Bacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA Deposited 2022-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 60 PDB declaration: 180-meric
Chain A 1–177（177 aa） Fragment：N-terminal domain (UNP residues 1-177)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.30 Å
7UJL Bacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA Deposited 2022-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–177（177 aa） Fragment：N-terminal domain (UNP residues 1-177)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.30 Å
8TFU Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 Deposited 2023-07-11 Different construct Different mutation/modification 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 182–261（80 aa）
Mutation：GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic
Resolution 1.48 Å R-free 0.220
8TFU Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic
Resolution 1.48 Å R-free 0.220
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 Deposited 2023-07-12 Different construct Different mutation/modification 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 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；2.0 M ammonium sulfate, 0.1 M Tris pH 8.6
Resolution 1.77 Å R-free 0.234
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；2.0 M ammonium sulfate, 0.1 M Tris pH 8.6
Resolution 1.77 Å R-free 0.234
8TG8 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 3 Deposited 2023-07-12 Different construct Different mutation/modification 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 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.6
Resolution 1.58 Å R-free 0.232
8TGC Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：N-TERMINAL GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.4 M ammonium phosphate dibasic, 0.1M Tris pH 8.5
Resolution 1.48 Å R-free 0.259
8TGC Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 182–261（80 aa）
Mutation：N-TERMINAL GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.4 M ammonium phosphate dibasic, 0.1M Tris pH 8.5
Resolution 1.48 Å R-free 0.259

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VBET_LAMBD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–67； UniProt 194–260 Author chain E； PDBConstruct 1–67； UniProt 194–260 Author chain F； PDBConstruct 1–67； UniProt 194–260

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 6m9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m9k
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6m9k
Deposition date deposition_date2018-08-23
Structure title titleCrystal structure of lambda exonuclease in complex with the Red beta C-terminal domain
Keywords keywordsprotein-protein complex, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier33.30 Å
Radius of gyration Rg (electron density) rg_electron32.48 Å
Forward intensity I(0) i0163615000.00
Molecular weight molecular_weight99558.0 kDa
Excluded volume excluded_volume123500 ų
Envelope volume envelope_volume166330 ų
Hydration-shell volume shell_volume42158 ų
Envelope diameter envelope_diameter99.8 Å
Shell Rg shell_rg40.04 Å
Envelope Rg envelope_rg31.53 Å
Shape Rg shape_rg32.47 Å
Total Rg total_rg33.16 Å
Total atoms total_atoms6970
Residues n_residues873
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
▼

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

Maximum dimension Dmax dmax100.7 Å
Rg (real space) rg_real33.15 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real1.6360e+08
I(0) uncertainty (real space) i0_real_error2.1130e+06
Rg (reciprocal space) rg_reciprocal33.24 Å
I(0) (reciprocal space) i0_reciprocal163600000.0000
Solution quality estimate total_estimate0.9109
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.3 Å
Skewness Skewness skewness0.060
Kurtosis Kurtosis kurtosis-0.683
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha56120000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.940
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6m9ka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease
Domain ID domain_idd6m9kb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease
Domain ID domain_idd6m9kc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease

CATH v4.4 (3 domains)

Domain ID domain_id6m9kA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
Domain ID domain_id6m9kB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
Domain ID domain_id6m9kC00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
▶

8. Citations (1)

▶

9. Files and Curves (10)