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- PDB-4x36: Crystal structure of the autolysin LytA from Streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4x36
TitleCrystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4
ComponentsAutolysin
KeywordsHYDROLASE / Autolysin / amidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Cholin Binding / left handed beta-beta-3-solenoid / Lysozyme-like / Peptidoglycan recognition protein-like / Choline-binding repeat / Ami_2 / N-acetylmuramoyl-L-alanine amidase / Putative cell wall binding repeat / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily ...Cholin Binding / left handed beta-beta-3-solenoid / Lysozyme-like / Peptidoglycan recognition protein-like / Choline-binding repeat / Ami_2 / N-acetylmuramoyl-L-alanine amidase / Putative cell wall binding repeat / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Cell wall-binding repeat profile. / Cell wall/choline-binding repeat / Ribbon / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / Autolysin
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.101 Å
AuthorsCheng, W. / Li, Q. / Zhou, C.Z. / Chen, Y.X.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2013CB835300 and 2014CB910100 China
National Natural Science Foundation of China31270781 and U1332114 China
Fundamental Research Funds for the Central Universities China
Program for Changjiang Scholars and Innovative Research Team in University China
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Full-length structure of the major autolysin LytA.
Authors: Li, Q. / Cheng, W. / Morlot, C. / Bai, X.H. / Jiang, Y.L. / Wang, W. / Roper, D.I. / Vernet, T. / Dong, Y.H. / Chen, Y. / Zhou, C.Z.
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,05313
Polymers36,9151
Non-polymers1,13912
Water4,342241
1
A: Autolysin
hetero molecules

A: Autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,10726
Polymers73,8292
Non-polymers2,27824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Unit cell
Length a, b, c (Å)101.282, 101.282, 119.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Autolysin / / Cell wall hydrolase / Mucopeptide aminohydrolase / Murein hydrolase / N-acetylmuramoyl-L-alanine amidase


Mass: 36914.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: lytA, SP_1937 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H14NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-tris propane pH 7.0, 1.3 M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012
RadiationMonochromator: Si(lll) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36872 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALAdata scaling
SOLVEphasing
RefinementResolution: 2.101→46.632 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1841 5 %
Rwork0.1828 --
obs0.1836 36808 99.78 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.531 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2994 Å20 Å2-0 Å2
2--5.2994 Å2-0 Å2
3----10.5988 Å2
Refinement stepCycle: LAST / Resolution: 2.101→46.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 72 241 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082753
X-RAY DIFFRACTIONf_angle_d1.0843732
X-RAY DIFFRACTIONf_dihedral_angle_d13.082982
X-RAY DIFFRACTIONf_chiral_restr0.076358
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.17610.26451800.24973426X-RAY DIFFRACTION100
2.1761-2.26320.26371710.23673448X-RAY DIFFRACTION100
2.2632-2.36620.26851770.23633437X-RAY DIFFRACTION100
2.3662-2.49090.25281870.21183463X-RAY DIFFRACTION100
2.4909-2.6470.24432050.21753436X-RAY DIFFRACTION100
2.647-2.85130.23961710.20623484X-RAY DIFFRACTION100
2.8513-3.13820.19271780.17673511X-RAY DIFFRACTION100
3.1382-3.59220.20081880.17763517X-RAY DIFFRACTION100
3.5922-4.52520.14632070.14343524X-RAY DIFFRACTION100
4.5252-46.64310.20551770.17273721X-RAY DIFFRACTION99

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