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- PDB-4s3j: Crystal structure of the Bacillus cereus spore cortex-lytic enzym... -

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Basic information

Entry
Database: PDB / ID: 4s3j
TitleCrystal structure of the Bacillus cereus spore cortex-lytic enzyme SleL
ComponentsCortical-lytic enzyme
KeywordsHYDROLASE / TIM Barrel / N-acetylglucosaminidase / Spore cortex
Function / homologyChitinase A; domain 3 - #10 / Chitinase A; domain 3 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Cortical-lytic enzyme
B: Cortical-lytic enzyme
C: Cortical-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7776
Polymers145,5903
Non-polymers1863
Water24,0681336
1
A: Cortical-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5301
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cortical-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5301
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cortical-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5301
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 62.730, 119.880
Angle α, β, γ (deg.)92.70, 100.99, 108.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cortical-lytic enzyme / LysM domain protein


Mass: 48530.141 Da / Num. of mol.: 3 / Fragment: UNP residues 2-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10876 / Gene: bcere0002_33520, DJ50_4346 / Plasmid: pNZ / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: C2N467
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M trisodium citrate buffer, pH 5.5, 20% (w/v) PEG 3,000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2013
RadiationMonochromator: Si(111) single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 182930 / Num. obs: 169576 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 18.74
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13527 / Rsym value: 0.52 / % possible all: 78.3

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Processing

Software
NameVersionClassification
GDAdata 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
Starting model: PDB entry 3CZ8

3cz8


Resolution: 1.6→47.811 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 1942 1.18 %Random
Rwork0.1568 ---
obs0.157 164510 89.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→47.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10143 0 12 1336 11491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910398
X-RAY DIFFRACTIONf_angle_d1.1814128
X-RAY DIFFRACTIONf_dihedral_angle_d12.4823832
X-RAY DIFFRACTIONf_chiral_restr0.051568
X-RAY DIFFRACTIONf_plane_restr0.0071820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63910.25551100.21838932X-RAY DIFFRACTION69
1.6391-1.68340.2451200.202910262X-RAY DIFFRACTION80
1.6834-1.7330.23391300.192310838X-RAY DIFFRACTION84
1.733-1.78890.20521340.185911374X-RAY DIFFRACTION88
1.7889-1.85290.20451420.1811685X-RAY DIFFRACTION91
1.8529-1.92710.20491370.178111731X-RAY DIFFRACTION91
1.9271-2.01480.21051390.173311461X-RAY DIFFRACTION89
2.0148-2.1210.19141430.16612134X-RAY DIFFRACTION94
2.121-2.25390.19021490.158712361X-RAY DIFFRACTION96
2.2539-2.42790.18261480.152812354X-RAY DIFFRACTION96
2.4279-2.67220.15061470.149412262X-RAY DIFFRACTION95
2.6722-3.05880.1581440.150212070X-RAY DIFFRACTION93
3.0588-3.85350.14951500.144612631X-RAY DIFFRACTION98
3.8535-47.83230.16721490.142812473X-RAY DIFFRACTION97
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)
11.52270.73950.06690.93140.12481.4285-0.0367-0.0749-0.05780.0026-0.03310.2096-0.1181-0.1479-0.00070.09860.0344-0.05670.1843-0.02360.172-27.1288-1.30894.6259
20.36410.2112-0.06050.5537-0.01620.49790.1171-0.0619-0.03590.2244-0.13480.08560.0307-0.0660.00210.1619-0.0501-0.00530.17750.01110.1223-24.15982.4731109.7693
30.40790.13660.08110.70150.15030.50510.1583-0.06220.09650.2978-0.20880.1175-0.14620.02150.0430.3045-0.07710.03490.1813-0.01720.1556-14.607332.7632115.5893
40.39970.1435-0.1780.83270.0720.73960.1183-0.0108-0.06420.238-0.1471-0.0497-0.05380.05310.00490.1169-0.0262-0.02620.13780.00870.1132-12.523111.4261106.3585
50.98270.38950.14830.59350.09440.18590.06340.25550.0293-0.23010.00440.1513-0.0297-0.1368-0.03010.15390.1109-0.09130.23580.01510.199-13.445663.169863.1321
60.1758-0.0843-0.0491.2115-0.27570.43680.08650.0670.0122-0.1801-0.06950.0316-0.0345-0.0491-0.01030.12940.0609-0.00360.16490.01980.17551.801157.812464.7751
70.5867-0.0420.15470.6634-0.03950.55420.05290.0143-0.1711-0.1028-0.08570.02440.10480.00350.02730.11530.0375-0.03180.14820.00090.20156.677427.172775.2002
80.2422-0.1072-0.06170.1890.0940.13830.0047-0.0742-0.05160.0073-0.0227-0.0720.03820.03020.00860.00340.061-0.05570.13290.00840.18877.430745.379882.3445
90.1934-0.06080.04380.1865-0.07480.18910.05250.0403-0.0354-0.1142-0.07240.07710.0392-0.0601-0.0165-0.01360.0777-0.05840.1551-0.01070.1583-6.645452.325775.1029
100.23680.13620.28261.2730.49830.4528-0.0473-0.0489-0.1856-0.19920.07280.040.0937-0.0274-0.03630.4406-0.01810.1030.17810.04440.2347-31.130921.273845.3132
110.26780.0524-0.14180.4744-0.01810.14130.03050.00260.0118-0.14380.0260.02110.1099-0.00430.08550.7555-0.12420.18810.1992-0.04790.2623-24.541925.164731.0966
120.31370.1984-0.19770.7642-0.24910.6089-0.0727-0.016-0.058-0.0105-0.0142-0.0514-0.17420.1294-0.1850.6754-0.14470.24330.2457-0.05910.3133-2.707748.06835.2415
130.19990.0118-0.15560.2818-0.20640.6505-0.03490.004-0.0326-0.0568-0.0109-0.0442-0.01430.0835-0.0450.7649-0.16030.28290.2693-0.06690.33050.143449.641725.0819
140.37210.0956-0.20720.0915-0.13940.2253-0.00950.04660.0175-0.12120.0685-0.0646-0.06590.01570.16830.7788-0.13220.20920.2187-0.02890.2277-18.671646.818525.4878
150.38860.234-0.41390.2108-0.10550.8807-0.01620.08740.0205-0.29670.0602-0.0139-0.0795-0.0134-0.0580.5747-0.08710.13310.1618-0.01620.1991-24.146245.631232.3315
160.4268-0.16220.02790.24210.14760.1481-0.10610.0242-0.0443-0.35680.1212-0.04310.0945-0.02170.10820.512-0.06180.12040.142-0.02150.1889-26.863435.975139.0125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:35 )A5 - 35
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:123 )A36 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:295 )A124 - 295
4X-RAY DIFFRACTION4( CHAIN A AND RESID 296:430 )A296 - 430
5X-RAY DIFFRACTION5( CHAIN B AND RESID 5:60 )B5 - 60
6X-RAY DIFFRACTION6( CHAIN B AND RESID 61:123 )B61 - 123
7X-RAY DIFFRACTION7( CHAIN B AND RESID 124:244 )B124 - 244
8X-RAY DIFFRACTION8( CHAIN B AND RESID 245:334 )B245 - 334
9X-RAY DIFFRACTION9( CHAIN B AND RESID 335:432 )B335 - 432
10X-RAY DIFFRACTION10( CHAIN C AND RESID 6:60 )C6 - 60
11X-RAY DIFFRACTION11( CHAIN C AND RESID 61:123 )C61 - 123
12X-RAY DIFFRACTION12( CHAIN C AND RESID 124:196 )C124 - 196
13X-RAY DIFFRACTION13( CHAIN C AND RESID 197:244 )C197 - 244
14X-RAY DIFFRACTION14( CHAIN C AND RESID 245:302 )C245 - 302
15X-RAY DIFFRACTION15( CHAIN C AND RESID 303:344 )C303 - 344
16X-RAY DIFFRACTION16( CHAIN C AND RESID 345:430 )C345 - 430

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