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- PDB-5jqc: Crystal structure putative autolysin from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 5jqc
TitleCrystal structure putative autolysin from Listeria monocytogenes
ComponentsLmo1076 protein
KeywordsHYDROLASE / autolysin / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


amidase activity / cell wall organization / extracellular region
Similarity search - Function
Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lmo1076 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.149 Å
AuthorsChang, C. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure putative autolysin from Listeria monocytogenes
Authors: Chang, C. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo1076 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7129
Polymers28,9351
Non-polymers7778
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.468, 89.323, 94.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lmo1076 protein


Mass: 28935.180 Da / Num. of mol.: 1 / Fragment: UNP residues 233-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo1076 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8Y842
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris hydrochloride, 40 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. obs: 17148 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.89

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Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.149→44.662 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.24
RfactorNum. reflection% reflection
Rfree0.2524 1517 4.87 %
Rwork0.1955 --
obs0.1984 17076 88.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.11 Å2 / Biso mean: 66.9282 Å2 / Biso min: 37.86 Å2
Refinement stepCycle: final / Resolution: 2.149→44.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 47 52 2016
Biso mean--93.12 60.12 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072021
X-RAY DIFFRACTIONf_angle_d0.8552729
X-RAY DIFFRACTIONf_chiral_restr0.052294
X-RAY DIFFRACTIONf_plane_restr0.005340
X-RAY DIFFRACTIONf_dihedral_angle_d12.1781168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1492-2.21850.3121980.26761714181257
2.2185-2.29780.3181880.25331985207364
2.2978-2.38980.30651200.25792206232674
2.3898-2.49860.37811450.28992679282488
2.4986-2.63030.34111290.30073057318699
2.6303-2.7950.37591520.25162993314599
2.795-3.01080.34311440.25153029317399
3.0108-3.31370.3341600.24922979313999
3.3137-3.7930.2551410.191430263167100
3.793-4.77790.21791630.14352978314198
4.7779-44.67110.18991770.16372972314998

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