4a8a

Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme

Method: ELECTRON MICROSCOPY Dmax: 158.6 Å Quality: GOOD

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

PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ

ESCHERICHIA COLI

UniProt P39099

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 × 13 PDB declaration: tridecameric(13) Consistent with protein copy count Chain A; UniProt 28–455 Chain B; UniProt 28–455 Chain C; UniProt 28–455 Chain D; UniProt 28–455 Chain E; UniProt 28–455 Chain F; UniProt 28–455 Chain G; UniProt 28–455 Chain H; UniProt 28–455 Chain I; UniProt 28–455 Chain J; UniProt 28–455 Chain K; UniProt 28–455 Chain L; UniProt 28–455 Mutation:YES LYSOZYME C × 1 (P00698) ELECTRON MICROSCOPY cryo-EM buffer:20 MM HEPES/NAOH, 150 MM NACL;pH 7.5;20 MM HEPES/NAOH, 150 MM NACL cryo-EM vitrification conditions:Cryogen ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, Resolution 14.20 Å

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.

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

View Construct and Data Evidence
UniProt name DEGQ_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–428; UniProt 28–455 Author chain B; PDBConstruct 1–428; UniProt 28–455 Author chain C; PDBConstruct 1–428; UniProt 28–455 Author chain D; PDBConstruct 1–428; UniProt 28–455 Author chain E; PDBConstruct 1–428; UniProt 28–455 Author chain F; PDBConstruct 1–428; UniProt 28–455 Author chain G; PDBConstruct 1–428; UniProt 28–455 Author chain H; PDBConstruct 1–428; UniProt 28–455 Author chain I; PDBConstruct 1–428; UniProt 28–455 Author chain J; PDBConstruct 1–428; UniProt 28–455 Author chain K; PDBConstruct 1–428; UniProt 28–455 Author chain L; PDBConstruct 1–428; UniProt 28–455

LYSOZYME C

OrganismNot specified

UniProt P00698

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 × 13 PDB declaration: tridecameric(13) Consistent with protein copy count Chain M; UniProt 19–147 Not recorded PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ × 12 (P39099) ELECTRON MICROSCOPY cryo-EM buffer:20 MM HEPES/NAOH, 150 MM NACL;pH 7.5;20 MM HEPES/NAOH, 150 MM NACL cryo-EM vitrification conditions:Cryogen ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, Resolution 14.20 Å

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.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 2
Chains and sequence ranges Author chain M; PDBConstruct 1–129; UniProt 19–147

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 4a8a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4a8a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4a8a
Deposition date deposition_date2011-11-20
Structure title titleAsymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme
Keywords keywordsHYDROLASE-HYDROLASE COMPLEX, CHAPERONE; HYDROLASE/HYDROLASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier62.84
Radius of gyration Rg (electron density) rg_electron62.01
Forward intensity I(0) i03360600000.00
Molecular weight molecular_weight493220.0 kDa
Excluded volume excluded_volume611090 ų
Envelope volume envelope_volume811960 ų
Hydration-shell volume shell_volume112930 ų
Envelope diameter envelope_diameter157.5
Shell Rg shell_rg68.57
Envelope Rg envelope_rg53.25
Shape Rg shape_rg61.84
Total Rg total_rg62.12
Total atoms total_atoms
Residues n_residues
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 dmax158.6
Rg (real space) rg_real62.01
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real3.3610e+09
I(0) uncertainty (real space) i0_real_error5.7490e+07
Rg (reciprocal space) rg_reciprocal63.53
I(0) (reciprocal space) i0_reciprocal3369000000.0000
Solution quality estimate total_estimate0.8065
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary101.5
Skewness Skewness skewness-0.408
Kurtosis Kurtosis kurtosis-0.595
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha195600000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)