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- PDB-6tci: The crystal structure of SleB N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6tci
TitleThe crystal structure of SleB N-terminal domain
ComponentsSpore cortex-lytic enzyme
KeywordsHYDROLASE / Spore cortex lytic enzyme / peptidoglycan binding domain
Function / homology
Function and homology information


intracellular immature spore / spore germination / sporulation resulting in formation of a cellular spore / cell wall organization / hydrolase activity
Similarity search - Function
Cell wall hydrolase, SleB / Spore cortex-lytic enzyme SleB / Cell wall hydrolase SleB, domain 1 / Cell Wall Hydrolase / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily ...Cell wall hydrolase, SleB / Spore cortex-lytic enzyme SleB / Cell wall hydrolase SleB, domain 1 / Cell Wall Hydrolase / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Spore cortex-lytic enzyme
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsChirgadze, D.Y. / Hardwick, S.W. / Christie, G.
CitationJournal: To Be Published
Title: The crystal structure of SleB N-terminal domain
Authors: Chirgadze, D.Y. / Hardwick, S.W. / Christie, G.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spore cortex-lytic enzyme


Theoretical massNumber of molelcules
Total (without water)8,2611
Polymers8,2611
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 43.330, 72.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Spore cortex-lytic enzyme / SCLE / Germination-specific amidase


Mass: 8261.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: sleB, BC_2753 / Plasmid: pET-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A3V0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350 containing 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.47→30.64 Å / Num. obs: 12245 / % possible obs: 99.45 % / Redundancy: 8.8 % / Biso Wilson estimate: 16.69 Å2 / CC1/2: 0.886 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.099 / Rrim(I) all: 0.079 / Net I/σ(I): 17.4
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.586 / Num. unique obs: 1128 / CC1/2: 0.637 / Rpim(I) all: 0.231 / Rrim(I) all: 0.16 / % possible all: 94.39

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LPQ

4lpq


Resolution: 1.47→30.64 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1335
RfactorNum. reflection% reflection
Rfree0.2179 924 7.55 %
Rwork0.1703 --
obs0.1738 12245 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.47→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 0 0 71 633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045574
X-RAY DIFFRACTIONf_angle_d0.6822774
X-RAY DIFFRACTIONf_chiral_restr0.065981
X-RAY DIFFRACTIONf_plane_restr0.0038100
X-RAY DIFFRACTIONf_dihedral_angle_d3.0053199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.550.25551320.15681525X-RAY DIFFRACTION96.11
1.55-1.640.18861410.14861560X-RAY DIFFRACTION100
1.64-1.770.22211420.14211579X-RAY DIFFRACTION100
1.77-1.950.19551140.1551622X-RAY DIFFRACTION100
1.95-2.230.21661250.16171620X-RAY DIFFRACTION100
2.23-2.810.23081350.19661656X-RAY DIFFRACTION100
2.81-30.640.2161350.17191759X-RAY DIFFRACTION100

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