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- PDB-3fi7: Crystal Structure of the autolysin Auto (Lmo1076) from Listeria m... -

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Basic information

Entry
Database: PDB / ID: 3fi7
TitleCrystal Structure of the autolysin Auto (Lmo1076) from Listeria monocytogenes, catalytic domain
ComponentsLmo1076 protein
KeywordsHYDROLASE / Listeria monocytogenes / autolysin / N acetylglucosaminidase / peptidoglycan hydrolase / autoinhibition / GH73
Function / homology
Function and homology information


amidase activity / cell wall organization / extracellular region
Similarity search - Function
DNA polymerase; domain 6 / 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. / Rhinovirus 14, subunit 4 / Lysozyme - #10 ...DNA polymerase; domain 6 / 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. / Rhinovirus 14, subunit 4 / Lysozyme - #10 / Lysozyme / Few Secondary Structures / Irregular / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBublitz, M. / Polle, L. / Holland, C. / Nimtz, M. / Heinz, D.W. / Schubert, W.D.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structural basis for autoinhibition and activation of Auto, a virulence-associated peptidoglycan hydrolase of Listeria monocytogenes.
Authors: Bublitz, M. / Polle, L. / Holland, C. / Heinz, D.W. / Nimtz, M. / Schubert, W.D.
History
DepositionDec 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Lmo1076 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8422
Polymers20,7461
Non-polymers961
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Lmo1076 protein
hetero molecules

A: Lmo1076 protein
hetero molecules

A: Lmo1076 protein
hetero molecules

A: Lmo1076 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3688
Polymers82,9844
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area11240 Å2
ΔGint-122 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.500, 133.500, 88.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Lmo1076 protein


Mass: 20745.906 Da / Num. of mol.: 1 / Fragment: fused residues 52-71 and 84-243
Source method: isolated from a genetically manipulated source
Details: A FUSION OF THREE NON-PHYSIOLOGICAL RESIDUES (GAM), LMO1076 52-71, LMO1076 84-243
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: EGD-e / Gene: lmo1076 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3) RIL
References: UniProt: Q8Y842, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN OF NON-PHYSIOLOGICAL RESIDUES (GAM), LMO1076 52-71, LMO1076 84-243. LOOP RESIDUES 72- ...FUSION PROTEIN OF NON-PHYSIOLOGICAL RESIDUES (GAM), LMO1076 52-71, LMO1076 84-243. LOOP RESIDUES 72-83 WERE DELETED BY MUTAGENESIS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.48 Å3/Da / Density % sol: 77.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1M ammonium sulfate, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2008 / Details: cylindrical grazing incidence mirror
RadiationMonochromator: cooled channel-cut silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 19770 / % possible obs: 99.2 % / Redundancy: 15.9 % / Biso Wilson estimate: 52.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 37.71
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 6.49 / Num. unique all: 1949 / Rsym value: 0.525 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→27.48 Å / SU ML: 0.3 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1003 5.14 %random
Rwork0.18 ---
obs0.181 19521 98.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.143 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 41.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.821 Å20 Å20 Å2
2--0.821 Å20 Å2
3----1.6419 Å2
Refinement stepCycle: LAST / Resolution: 2.35→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 5 158 1584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061468
X-RAY DIFFRACTIONf_angle_d0.8831993
X-RAY DIFFRACTIONf_chiral_restr0.063203
X-RAY DIFFRACTIONf_plane_restr0.003256
X-RAY DIFFRACTIONf_dihedral_angle_d16.015517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3512-2.47510.23581470.22672596259699
2.4751-2.63010.25421500.20472589258998
2.6301-2.8330.20221370.18182595259598
2.833-3.11770.20171340.1742642264299
3.1177-3.5680.18351420.16432672267299
3.568-4.49210.15441370.13432686268699
4.4921-27.47960.2021560.18512738273895
Refinement TLS params.Method: refined / Origin x: -65.9846 Å / Origin y: 14.1224 Å / Origin z: 16.6688 Å
111213212223313233
T0.2692 Å2-0.0015 Å2-0.0075 Å2-0.2549 Å2-0.017 Å2--0.2451 Å2
L0.4274 °2-0.085 °20.0182 °2-1.2405 °2-0.3142 °2--0.7002 °2
S-0.0125 Å °-0.0601 Å °0.0756 Å °0.1674 Å °0.0022 Å °-0.1069 Å °-0.1846 Å °0.0321 Å °0.0079 Å °
Refinement TLS groupSelection details: chain A

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