5npo

Promiscuous Protein Self-Assembly as a Function of Protein Stability

Method: X-RAY DIFFRACTION Dmax: 97.6 Å Quality: GOOD

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

Beta-lactamase TEM

Escherichia coli

UniProt P62593

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–286 Not recorded Beta-lactamase × 1 (D3INY1) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;292 K;7.5% PEG 6000, 0.1M MgCl2 and 0.05M Sodium acetate pH=5.5 Resolution 1.95 Å R-free 0.256

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.

72 other PDB entries and 155 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLAT_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–264; UniProt 24–286

Beta-lactamase

Escherichia coli

UniProt D3INY1

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 23–286 Not recorded Beta-lactamase TEM × 1 (P62593) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;292 K;7.5% PEG 6000, 0.1M MgCl2 and 0.05M Sodium acetate pH=5.5 Resolution 1.95 Å R-free 0.256

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name D3INY1_ECOLX
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–264; UniProt 23–286

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 5npo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5npo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5npo
Deposition date deposition_date2017-04-18
Structure title titlePromiscuous Protein Self-Assembly as a Function of Protein Stability
Keywords keywordsTEM1 beta-lactamase Hetrodimer, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.11
Radius of gyration Rg (electron density) rg_electron26.39
Forward intensity I(0) i046873900.00
Molecular weight molecular_weight52829.0 kDa
Excluded volume excluded_volume65965 ų
Envelope volume envelope_volume78649 ų
Hydration-shell volume shell_volume25995 ų
Envelope diameter envelope_diameter103.5
Shell Rg shell_rg32.07
Envelope Rg envelope_rg26.71
Shape Rg shape_rg26.40
Total Rg total_rg26.93
Total atoms total_atoms3706
Residues n_residues486
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 dmax97.6
Rg (real space) rg_real27.35
Rg uncertainty (real space) rg_real_error0.99
I(0) (real space) i0_real4.6870e+07
I(0) uncertainty (real space) i0_real_error8.0030e+05
Rg (reciprocal space) rg_reciprocal27.28
I(0) (reciprocal space) i0_reciprocal46870000.0000
Solution quality estimate total_estimate0.8070
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5
Skewness Skewness skewness0.567
Kurtosis Kurtosis kurtosis-0.140
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11620000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.637; Smooth: 0.953

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5npoa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase
Domain ID domain_idd5npob1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase
Domain ID domain_idd5npob2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id5npoA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id5npoB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily

8. Citations (1)

9. Files and Curves (10)