1pqk

Repacking of the Core of T4 Lysozyme by Automated Design

Method: X-RAY DIFFRACTION Dmax: 90.2 Å Quality: REASONABLE

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

Lysozyme

Enterobacteria phage T4

UniProt P00720

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 1–164 Mutation:C54T, G77A, I78V, C97A, L118I, M120Y, L133F, V149I, T152V No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.7;277 K;Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70 Resolution 2.00 Å R-free 0.277
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–164 Mutation:C54T, G77A, I78V, C97A, L118I, M120Y, L133F, V149I, T152V No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.7;277 K;Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70 Resolution 2.00 Å R-free 0.277
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–164 Mutation:C54T, G77A, I78V, C97A, L118I, M120Y, L133F, V149I, T152V No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.7;277 K;Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70 Resolution 2.00 Å R-free 0.277

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.

721 other PDB entries and 844 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–164; UniProt 1–164 Author chain B; PDBConstruct 1–164; UniProt 1–164 Author chain C; PDBConstruct 1–164; UniProt 1–164

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 1pqk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pqk
Deposition date deposition_date2003-06-18
Structure title titleRepacking of the Core of T4 Lysozyme by Automated Design
Keywords keywords;HYDROLASE (O-GLYCOSYL), T4 LYSOZYME, DESIGNED CORE MUTANT, AUTOMATED PROTEIN DESIGN, PROTEIN ENGINEERING, PROTEIN FOLDING, PROTEIN STABILITY, CORE REPACKING, BACK REVERTANT, DEAD-END ELIMINATION THEOREM, SIDE-CHAIN PACKING, OPTIMIZED ROTAMER COMBINATIONS, ORBIT, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.09
Radius of gyration Rg (electron density) rg_electron26.35
Forward intensity I(0) i051371400.00
Molecular weight molecular_weight56017.0 kDa
Excluded volume excluded_volume70357 ų
Envelope volume envelope_volume84433 ų
Hydration-shell volume shell_volume27672 ų
Envelope diameter envelope_diameter91.5
Shell Rg shell_rg32.56
Envelope Rg envelope_rg26.22
Shape Rg shape_rg26.34
Total Rg total_rg27.04
Total atoms total_atoms3948
Residues n_residues492
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 dmax90.2
Rg (real space) rg_real27.14
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real5.1370e+07
I(0) uncertainty (real space) i0_real_error6.8750e+05
Rg (reciprocal space) rg_reciprocal27.13
I(0) (reciprocal space) i0_reciprocal51370000.0000
Solution quality estimate total_estimate0.6708
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.1
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11360000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 0.089; Positv: 1.000; Valcen: 0.936; Smooth: 0.883

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1pqka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.3 — Phage lysozyme
Domain ID domain_idd1pqkb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.3 — Phage lysozyme
Domain ID domain_idd1pqkc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.3 — Phage lysozyme

CATH v4.4 (3 domains)

Domain ID domain_id1pqkA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id1pqkB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id1pqkC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)