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- PDB-5jen: Crystal structure of the anti-sigma factor RsiV bound to lysozyme -

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Basic information

Entry
Database: PDB / ID: 5jen
TitleCrystal structure of the anti-sigma factor RsiV bound to lysozyme
Components
  • Anti-sigma-V factor RsiV
  • Lysozyme C
KeywordsHYDROLASE/HYDROLASE RECEPTOR / Anti-sigma factor / Inhibitor / Receptor / HYDROLASE-HYDROLASE RECEPTOR complex
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / membrane => GO:0016020 / defense response to Gram-positive bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / membrane => GO:0016020 / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Lysozyme - #10 ...Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Anti-sigma-V factor RsiV / Lysozyme C
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGakhar, L. / Williams, K.B. / Ellermeir, C.D.
CitationJournal: To Be Published
Title: The anti-sigma factor RsiV is a receptor for lysozyme: The crystal structure of RsiV-lysozyme complex
Authors: Hastie, J.L. / Williams, K.B. / Gakhar, L. / Houtman, J.C. / Ellermeier, C.D.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-sigma-V factor RsiV
B: Lysozyme C
C: Anti-sigma-V factor RsiV
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,51512
Polymers92,3064
Non-polymers2098
Water7,044391
1
A: Anti-sigma-V factor RsiV
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2576
Polymers46,1532
Non-polymers1044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-46 kcal/mol
Surface area15790 Å2
MethodPISA
2
C: Anti-sigma-V factor RsiV
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2576
Polymers46,1532
Non-polymers1044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-45 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.213, 130.326, 136.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Anti-sigma-V factor RsiV


Mass: 31690.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rsiV, yrhM, BSU27130 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lambda DE3 / References: UniProt: O05403
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14462.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium nitrate, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→60.53 Å / Num. obs: 36905 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSVERSION January 10, 2014data reduction
XDSVERSION January 10, 2014data scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.166 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.2366 1812 4.92 %
Rwork0.1809 --
obs0.1837 36825 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 8 391 5796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145502
X-RAY DIFFRACTIONf_angle_d1.1597438
X-RAY DIFFRACTIONf_dihedral_angle_d14.2143366
X-RAY DIFFRACTIONf_chiral_restr0.061824
X-RAY DIFFRACTIONf_plane_restr0.007949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.39781480.2782637X-RAY DIFFRACTION100
2.3622-2.43170.30821490.22962614X-RAY DIFFRACTION100
2.4317-2.51020.2851470.20562677X-RAY DIFFRACTION100
2.5102-2.59990.32711450.19842597X-RAY DIFFRACTION100
2.5999-2.7040.2481060.18822712X-RAY DIFFRACTION100
2.704-2.82710.23481240.19212713X-RAY DIFFRACTION100
2.8271-2.97610.25531450.20142641X-RAY DIFFRACTION100
2.9761-3.16250.28091300.20842663X-RAY DIFFRACTION100
3.1625-3.40660.25881250.20362700X-RAY DIFFRACTION100
3.4066-3.74930.23891500.18412706X-RAY DIFFRACTION100
3.7493-4.29150.23111270.15532725X-RAY DIFFRACTION100
4.2915-5.40560.1651790.13362719X-RAY DIFFRACTION100
5.4056-47.17550.16931370.15472909X-RAY DIFFRACTION100

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