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- PDB-4s3k: Crystal structure of the Bacillus megaterium QM B1551 spore corte... -

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Basic information

Entry
Database: PDB / ID: 4s3k
TitleCrystal structure of the Bacillus megaterium QM B1551 spore cortex-lytic enzyme SleL
ComponentsSpore germination protein YaaHGermination
KeywordsHYDROLASE / TIM Barrel / N-acetylglucosaminidase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / chitin binding / carbohydrate metabolic process
Similarity search - Function
CFLE, GH18 catalytic domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / Chitinase A; domain 3 - #10 / LysM domain / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...CFLE, GH18 catalytic domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / Chitinase A; domain 3 - #10 / LysM domain / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Spore germination protein YaaH
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChristie, G. / Chirgadze, D.Y. / Ustok, F.I.
CitationJournal: Proteins / Year: 2015
Title: Structural and functional analysis of SleL, a peptidoglycan lysin involved in germination of Bacillus spores.
Authors: Ustok, F.I. / Chirgadze, D.Y. / Christie, G.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Spore germination protein YaaH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4533
Polymers49,2611
Non-polymers1922
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.439, 80.496, 90.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spore germination protein YaaH / Germination


Mass: 49261.215 Da / Num. of mol.: 1 / Fragment: UNP residues 2-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ATCC 12872 / QMB1551 / Gene: 8984459 (BMQ_0021), BMQ_0021, yaaH / Plasmid: pNZ / Production host: Lactococcus lactis (lactic acid bacteria)
References: UniProt: D5DUS2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium sulfate, 20% (w/v) PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2014
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→43.63 Å / Num. all: 51363 / Num. obs: 51055 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7431 / Rsym value: 0.725 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX(phenix.refine: 1.9_1692)model building
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.248 Å / SU ML: 0.14 / σ(F): 1.45 / Phase error: 16.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 2000 3.92 %Random
Rwork0.1672 ---
obs0.1679 50990 98.85 %-
all-51583 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 10 441 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043485
X-RAY DIFFRACTIONf_angle_d0.8644721
X-RAY DIFFRACTIONf_dihedral_angle_d12.4661311
X-RAY DIFFRACTIONf_chiral_restr0.036511
X-RAY DIFFRACTIONf_plane_restr0.005615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74260.271390.26273402X-RAY DIFFRACTION98
1.7426-1.78970.27481420.24823477X-RAY DIFFRACTION99
1.7897-1.84230.25281410.22573463X-RAY DIFFRACTION99
1.8423-1.90180.2441410.20723454X-RAY DIFFRACTION99
1.9018-1.96980.18691420.18183466X-RAY DIFFRACTION99
1.9698-2.04860.17661420.17053470X-RAY DIFFRACTION99
2.0486-2.14190.18841400.16123452X-RAY DIFFRACTION99
2.1419-2.25480.19821430.15293501X-RAY DIFFRACTION99
2.2548-2.39610.18361430.15353499X-RAY DIFFRACTION99
2.3961-2.5810.17621430.15813509X-RAY DIFFRACTION99
2.581-2.84070.17151440.16263517X-RAY DIFFRACTION99
2.8407-3.25160.15561440.15673534X-RAY DIFFRACTION99
3.2516-4.0960.16351460.15273564X-RAY DIFFRACTION99
4.096-40.25930.17981500.15723682X-RAY DIFFRACTION98
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)
10.23780.0094-0.0520.0776-0.04770.17090.01170.0099-0.01410.0688-0.0303-0.0429-0.06650.0845-0.01510.1453-0.015-0.02560.13680.01590.139252.300129.029684.7644
20.34990.0193-0.03240.2177-0.28390.441-0.57310.36650.3907-0.3970.03150.162-0.04440.4962-0.38640.4657-0.0138-0.16550.3845-0.01250.299554.452648.962191.2799
30.99870.0961-0.20230.7706-0.2210.4593-0.01670.1140.0205-0.05810.02940.05490.023-0.0477-0.00010.1230.0042-0.00410.13090.00360.096619.122829.939368.9989
40.3823-0.0234-0.17610.46880.07120.7575-0.03150.1441-0.0581-0.09620.0018-0.10820.0223-0.07470.02010.1182-0.02190.01140.1304-0.02360.145946.411918.969365.4839
50.2832-0.02540.08950.06750.01450.1567-0.03420.0088-0.00350.06580.0202-0.0341-0.05150.011-0.00430.1303-0.0016-0.00260.11310.00150.140634.457134.855877.3315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:48 )A-2 - 48
2X-RAY DIFFRACTION2( CHAIN A AND RESID 49:98 )A49 - 98
3X-RAY DIFFRACTION3( CHAIN A AND RESID 99:323 )A99 - 323
4X-RAY DIFFRACTION4( CHAIN A AND RESID 324:384 )A324 - 384
5X-RAY DIFFRACTION5( CHAIN A AND RESID 385:430 )A385 - 430

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