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- PDB-4fet: Catalytic domain of germination-specific lytic tansglycosylase Sl... -

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Basic information

Entry
Database: PDB / ID: 4fet
TitleCatalytic domain of germination-specific lytic tansglycosylase SleB from Bacillus anthracis
ComponentsSpore cortex-lytic enzyme prepeptide
KeywordsHYDROLASE / transglycosylase / cortex hydrolase domain / Sodium Ion / SeMet / cortex
Function / homology
Function and homology information


asexual sporulation / spore germination / sporulation resulting in formation of a cellular spore / catalytic activity / cell wall organization / lysozyme 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
Spore cortex-lytic enzyme / Spore cortex-lytic enzyme
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.909 Å
AuthorsJing, X. / Heffron, J. / Popham, D.L. / Schubot, F.D.
CitationJournal: Proteins / Year: 2012
Title: The catalytic domain of the germination-specific lytic transglycosylase SleB from Bacillus anthracis displays a unique active site topology.
Authors: Jing, X. / Robinson, H.R. / Heffron, J.D. / Popham, D.L. / Schubot, F.D.
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Spore cortex-lytic enzyme prepeptide
A: Spore cortex-lytic enzyme prepeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7884
Polymers48,7422
Non-polymers462
Water4,468248
1
B: Spore cortex-lytic enzyme prepeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3942
Polymers24,3711
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Spore cortex-lytic enzyme prepeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3942
Polymers24,3711
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.850, 64.450, 84.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B131 - 253
2111A132 - 253
1121B301
2121A301

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999994, 0.000209, -0.003374), (0.000226, -0.999987, 0.005006), (-0.003373, -0.005007, -0.999982)27.00371, -8.23305, 41.59853

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Components

#1: Protein Spore cortex-lytic enzyme prepeptide


Mass: 24370.908 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 125-253) / Mutation: L143M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sleB, BA_2748, BAS2562, GBAA_2748 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81PQ3, UniProt: A0A6L8PLE1*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 1.5 Å3/Da / Density % sol: 17.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: 1:1 mixture of 2.5 mg/mL protein and a crystallization solution composed of 0.2M ammonium sulfate, 0.1M Bis-Tris (pH 5.8) and 15% w/v polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9792
SYNCHROTRONNSLS X29A20.9611, 0.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 21, 2011
ADSC QUANTUM 3152CCDDec 1, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.96111
30.97941
ReflectionResolution: 1.909→32.22 Å / Num. obs: 23345 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.909→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CCP4refinement
PHENIXmodel building
REFMAC5.6.0117refinement
CCP4data reduction
CCP4data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.909→32.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.252 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24867 1211 5.2 %RANDOM
Rwork0.20269 ---
obs0.20511 22134 99.85 %-
all-22136 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.474 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.909→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 2 248 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9392657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29824.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15515283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.441158
X-RAY DIFFRACTIONr_chiral_restr0.1830.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDNumberRms dev position (Å)
19442.04
210.28
LS refinement shellResolution: 1.909→1.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 72 -
Rwork0.219 1486 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6266-0.1343-0.070.96340.45390.21450.00860.0054-0.01190.0149-0.0051-0.00720.00380.0004-0.00350.04160.0043-0.00460.0360.00020.00183.74731.04325.4017
20.88130.41290.10090.98860.43550.24260.01240.0286-0.01960.0017-0.01350.0588-0.00490.01240.0010.023-0.00250.00430.029-0.00410.0408-23.1498-9.114716.4697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B131 - 253
2X-RAY DIFFRACTION2A132 - 253

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