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- PDB-8c4d: N-acetylmuramoyl-L-alanine amidase from Enterococcus faecium prop... -

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Basic information

Entry
Database: PDB / ID: 8c4d
TitleN-acetylmuramoyl-L-alanine amidase from Enterococcus faecium prophage genome
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsANTIMICROBIAL PROTEIN / Enterococcus faecium / antibacterial / enzyme engineering / enzybiotics
Function / homologyCITRATE ANION
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPapageorgiou, A.C. / Premetis, G.E. / Labrou, N.E.
Funding support Greece, European Union, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)4036 Greece
iNEXT-Discovery22231European Union
CitationJournal: Sci Rep / Year: 2023
Title: Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium.
Authors: Premetis, G.E. / Stathi, A. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionJan 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,63010
Polymers37,1641
Non-polymers4659
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-106 kcal/mol
Surface area8250 Å2
Unit cell
Length a, b, c (Å)74.713, 74.713, 133.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetylmuramoyl-L-alanine amidase


Mass: 37164.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The crystals contained only the amidase domain. The rest of the expressed protein was probably removed by proteolysis.
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: HV425_06660 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.84 % / Description: Small (<0.15 mm) rod-like crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 3000, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.97→49.73 Å / Num. obs: 27661 / % possible obs: 99.9 % / Redundancy: 25.5 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.46 / Net I/σ(I): 9
Reflection shellResolution: 1.97→2.03 Å / Num. unique obs: 2614 / CC1/2: 0.42 / Rrim(I) all: 4.63 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→49.73 Å / SU ML: 0.2098 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 1988 7.21 %
Rwork0.1734 25580 -
obs0.1749 27568 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.56 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 21 190 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781529
X-RAY DIFFRACTIONf_angle_d0.87762079
X-RAY DIFFRACTIONf_chiral_restr0.057219
X-RAY DIFFRACTIONf_plane_restr0.0096278
X-RAY DIFFRACTIONf_dihedral_angle_d22.4276214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.30371340.29951720X-RAY DIFFRACTION97.27
2.01-2.070.35031400.27071799X-RAY DIFFRACTION99.85
2.07-2.130.27331380.23691786X-RAY DIFFRACTION99.95
2.13-2.20.27821420.22481807X-RAY DIFFRACTION99.85
2.2-2.280.23111400.21271798X-RAY DIFFRACTION99.95
2.28-2.370.22571380.1951796X-RAY DIFFRACTION100
2.37-2.480.21341430.18441814X-RAY DIFFRACTION100
2.48-2.610.21681420.17461818X-RAY DIFFRACTION100
2.61-2.770.20081410.16851828X-RAY DIFFRACTION99.95
2.77-2.980.181410.16311825X-RAY DIFFRACTION100
2.98-3.280.18371440.16391841X-RAY DIFFRACTION100
3.28-3.760.16331440.13811856X-RAY DIFFRACTION100
3.76-4.730.16381460.12871882X-RAY DIFFRACTION99.41
4.74-49.730.17171550.18922010X-RAY DIFFRACTION99.82

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