4a8b

Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes

Method: ELECTRON MICROSCOPY Dmax: 159.9 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 × 18 PDB declaration: octadecameric(18) 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 × 6 (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 13.00 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 × 18 PDB declaration: octadecameric(18) Consistent with protein copy count Chain M; UniProt 19–147 Chain N; UniProt 19–147 Chain O; UniProt 19–147 Chain P; UniProt 19–147 Chain Q; UniProt 19–147 Chain R; 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 13.00 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 Author chain N; PDBConstruct 1–129; UniProt 19–147 Author chain O; PDBConstruct 1–129; UniProt 19–147 Author chain P; PDBConstruct 1–129; UniProt 19–147 Author chain Q; PDBConstruct 1–129; UniProt 19–147 Author chain R; 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 4a8b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4a8b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4a8b
Deposition date deposition_date2011-11-20
Structure title titleSymmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes
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_guinier59.69
Radius of gyration Rg (electron density) rg_electron59.44
Forward intensity I(0) i04493890000.00
Molecular weight molecular_weight562840.0 kDa
Excluded volume excluded_volume694650 ų
Envelope volume envelope_volume855960 ų
Hydration-shell volume shell_volume123890 ų
Envelope diameter envelope_diameter158.2
Shell Rg shell_rg62.51
Envelope Rg envelope_rg52.82
Shape Rg shape_rg59.44
Total Rg total_rg59.50
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 dmax159.9
Rg (real space) rg_real59.10
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real4.4940e+09
I(0) uncertainty (real space) i0_real_error7.2000e+07
Rg (reciprocal space) rg_reciprocal60.16
I(0) (reciprocal space) i0_reciprocal4501000000.0000
Solution quality estimate total_estimate0.8400
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary79.9
Skewness Skewness skewness-0.135
Kurtosis Kurtosis kurtosis-0.650
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0004
Highest regularization parameter α highest_alpha331000000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; 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)