4ml7

Crystal structure of Brucella abortus PliC in complex with human lysozyme

Method: X-RAY DIFFRACTION Dmax: 72.2 Å Quality: EXCELLENT

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

Lysozyme C

Homo sapiens

UniProt P61626

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 19–148 Fragment:UNP residues 19-148 Humanlysozyme × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;287.15 K;0.1M sodium citrate tribasic, 40% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K Resolution 1.80 Å R-free 0.222
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 19–148 Fragment:UNP residues 19-148 Humanlysozyme × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;287.15 K;0.1M sodium citrate tribasic, 40% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K Resolution 1.80 Å R-free 0.222

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.

201 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–130; UniProt 19–148 Author chain C; PDBConstruct 1–130; UniProt 19–148

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 4ml7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ml7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ml7
Deposition date deposition_date2013-09-06
Structure title titleCrystal structure of Brucella abortus PliC in complex with human lysozyme
Keywords keywordsinhibitor, lysozyme, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.65
Radius of gyration Rg (electron density) rg_electron22.61
Forward intensity I(0) i045437500.00
Molecular weight molecular_weight50421.0 kDa
Excluded volume excluded_volume62408 ų
Envelope volume envelope_volume72612 ų
Hydration-shell volume shell_volume26612 ų
Envelope diameter envelope_diameter74.5
Shell Rg shell_rg30.04
Envelope Rg envelope_rg22.73
Shape Rg shape_rg22.54
Total Rg total_rg23.65
Total atoms total_atoms3534
Residues n_residues455
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 dmax72.2
Rg (real space) rg_real23.55
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real4.5440e+07
I(0) uncertainty (real space) i0_real_error5.5860e+05
Rg (reciprocal space) rg_reciprocal23.58
I(0) (reciprocal space) i0_reciprocal45440000.0000
Solution quality estimate total_estimate0.9123
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2
Skewness Skewness skewness0.220
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9840000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ml7a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme
Domain ID domain_idd4ml7c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme

CATH v4.4 (4 domains)

Domain ID domain_id4ml7A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4ml7B01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily200 — C-type lysozyme inhibitor
Domain ID domain_id4ml7C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4ml7D01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily200 — C-type lysozyme inhibitor

8. Citations (1)

9. Files and Curves (10)