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- PDB-4f55: Crystal Structure of the Catalytic Domain of the Bacillus cereus ... -

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Basic information

Entry
Database: PDB / ID: 4f55
TitleCrystal Structure of the Catalytic Domain of the Bacillus cereus SleB Protein
ComponentsSpore cortex-lytic enzyme
KeywordsHYDROLASE / lytic transglycosylase
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, domain 1 / Alpha-Beta Plaits - #60 / Cell wall hydrolase, SleB / Spore cortex-lytic enzyme SleB / Cell wall hydrolase SleB, domain 1 / Cell Wall Hydrolase / Alpha-Beta Plaits / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain ...Cell wall hydrolase SleB, domain 1 / Alpha-Beta Plaits - #60 / Cell wall hydrolase, SleB / Spore cortex-lytic enzyme SleB / Cell wall hydrolase SleB, domain 1 / Cell Wall Hydrolase / Alpha-Beta Plaits / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Other non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Spore cortex-lytic enzyme
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHao, B.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Crystal Structure of the Catalytic Domain of the Bacillus cereus SleB Protein, Important in Cortex Peptidoglycan Degradation during Spore Germination.
Authors: Li, Y. / Jin, K. / Setlow, B. / Setlow, P. / Hao, B.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spore cortex-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1924
Polymers13,9071
Non-polymers2853
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.626, 134.626, 134.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

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


Mass: 13906.643 Da / Num. of mol.: 1 / Fragment: the catalytic domain, UNP residues 136-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579/DSM 31 / Gene: BC_2753, sleB / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3V0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.8 M ammonium phosphate and 0.05 sodium citrate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 18099 / Num. obs: 18099 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 47.1 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 48.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 47.2 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 8.9 / Num. unique all: 885 / Rsym value: 0.555 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→47.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.793 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21172 912 5 %RANDOM
Rwork0.17964 ---
all0.18 18099 --
obs0.18121 17164 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.398 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 15 151 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221108
X-RAY DIFFRACTIONr_bond_other_d0.0010.02727
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9531528
X-RAY DIFFRACTIONr_angle_other_deg0.97931774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70623.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57815167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.399157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_mcbond_it2.0373695
X-RAY DIFFRACTIONr_mcbond_other0.6393279
X-RAY DIFFRACTIONr_mcangle_it351136
X-RAY DIFFRACTIONr_scbond_it5.0518413
X-RAY DIFFRACTIONr_scangle_it6.46811392
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 59 -
Rwork0.223 1237 -
obs-855 100 %
Refinement TLS params.Method: refined / Origin x: 54.4172 Å / Origin y: 45.3415 Å / Origin z: 28.6188 Å
111213212223313233
T0.0316 Å20.0087 Å20.05 Å2-0.0267 Å20.0152 Å2--0.1084 Å2
L2.6682 °2-0.889 °2-0.365 °2-3.2492 °2-0.1471 °2--0.3952 °2
S0.1805 Å °0.177 Å °0.1662 Å °-0.2287 Å °-0.1581 Å °-0.4565 Å °-0.0523 Å °0.0224 Å °-0.0224 Å °

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