5jen

Crystal structure of the anti-sigma factor RsiV bound to lysozyme

Method: X-RAY DIFFRACTION Dmax: 93.2 Å Quality: EXCELLENT

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

Anti-sigma-V factor RsiV

Bacillus subtilis (strain 168)

UniProt O05403

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 60–285 Non-standard monomer:Yes (specific site not provided by mmCIF) Lysozyme C × 1 (P00698) NA SODIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M sodium nitrate, 20% (w/v) PEG 3350. Resolution 2.30 Å R-free 0.237
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 60–285 Non-standard monomer:Yes (specific site not provided by mmCIF) Lysozyme C × 1 (P00698) NA SODIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M sodium nitrate, 20% (w/v) PEG 3350. Resolution 2.30 Å R-free 0.237

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 RSIV_BACSU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 46–271; UniProt 60–285 Author chain C; PDBConstruct 46–271; UniProt 60–285

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 19–147 Not recorded Anti-sigma-V factor RsiV × 1 (O05403) NA SODIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M sodium nitrate, 20% (w/v) PEG 3350. Resolution 2.30 Å R-free 0.237
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 19–147 Not recorded Anti-sigma-V factor RsiV × 1 (O05403) NA SODIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M sodium nitrate, 20% (w/v) PEG 3350. Resolution 2.30 Å R-free 0.237

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 1449 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 B; PDBConstruct 2–130; UniProt 19–147 Author chain D; PDBConstruct 2–130; 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 5jen

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5jen
Deposition date deposition_date2016-04-18
Structure title titleCrystal structure of the anti-sigma factor RsiV bound to lysozyme
Keywords keywordsAnti-sigma factor, Inhibitor, Receptor, HYDROLASE-HYDROLASE RECEPTOR complex; HYDROLASE/HYDROLASE RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.05
Radius of gyration Rg (electron density) rg_electron29.29
Forward intensity I(0) i098636900.00
Molecular weight molecular_weight77278.0 kDa
Excluded volume excluded_volume96245 ų
Envelope volume envelope_volume121770 ų
Hydration-shell volume shell_volume34612 ų
Envelope diameter envelope_diameter93.8
Shell Rg shell_rg36.58
Envelope Rg envelope_rg28.98
Shape Rg shape_rg29.29
Total Rg total_rg29.96
Total atoms total_atoms10724
Residues n_residues667
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 dmax93.2
Rg (real space) rg_real29.97
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real9.8640e+07
I(0) uncertainty (real space) i0_real_error1.4610e+06
Rg (reciprocal space) rg_reciprocal30.00
I(0) (reciprocal space) i0_reciprocal98640000.0000
Solution quality estimate total_estimate0.9120
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.2
Skewness Skewness skewness0.174
Kurtosis Kurtosis kurtosis-0.646
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19070000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5jenb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.0 — automated matches
Domain ID domain_idd5jend_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id5jenA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily40 — Fervidobacterium nodosum Rt17-B1 like
Domain ID domain_id5jenA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily20 — Heat-shock cognate protein, ATPase
Domain ID domain_id5jenB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id5jenC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily40 — Fervidobacterium nodosum Rt17-B1 like
Domain ID domain_id5jenC02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily20 — Heat-shock cognate protein, ATPase
Domain ID domain_id5jenD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)