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- PDB-7agm: Crystal structure of the N-acetylmuramyl-L-alanine amidase, Ami1,... -

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Basic information

Entry
Database: PDB / ID: 7agm
TitleCrystal structure of the N-acetylmuramyl-L-alanine amidase, Ami1, from Mycobacterium smegmatis
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsSUGAR BINDING PROTEIN / amidase / peptidoglycan
Function / homology: / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding / N-acetylmuramoyl-L-alanine amidase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBlaise, M. / Alsarraf, M.A.B.
CitationJournal: Cells / Year: 2020
Title: Functional Characterization of the N -Acetylmuramyl-l-Alanine Amidase, Ami1, from Mycobacterium abscessus .
Authors: Kussau, T. / Van Wyk, N. / Johansen, M.D. / Alsarraf, H.M.A.B. / Neyret, A. / Hamela, C. / Sorensen, K.K. / Thygesen, M.B. / Beauvineau, C. / Kremer, L. / Blaise, M.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,4964
Polymers47,3652
Non-polymers1312
Water8,143452
1
A: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7482
Polymers23,6831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7482
Polymers23,6831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.850, 68.840, 63.720
Angle α, β, γ (deg.)90.000, 91.866, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 23682.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6281 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: A0R5R2, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 17% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.35→63.6 Å / Num. obs: 79198 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 15.45 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 1.35→1.39 Å / Num. unique obs: 8163 / CC1/2: 0.6 / Rrim(I) all: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AGL

7agl


Resolution: 1.35→46.75 Å / SU ML: 0.1696 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1806 3960 5 %
Rwork0.1559 75214 -
obs0.1571 79174 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.24 Å2
Refinement stepCycle: LAST / Resolution: 1.35→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 2 452 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463293
X-RAY DIFFRACTIONf_angle_d0.76874488
X-RAY DIFFRACTIONf_chiral_restr0.0692489
X-RAY DIFFRACTIONf_plane_restr0.0056619
X-RAY DIFFRACTIONf_dihedral_angle_d11.84771220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.34461390.29442650X-RAY DIFFRACTION99.82
1.37-1.380.30551420.28542688X-RAY DIFFRACTION99.86
1.38-1.40.31821400.27292665X-RAY DIFFRACTION99.93
1.4-1.420.27461410.25552675X-RAY DIFFRACTION99.82
1.42-1.440.30581420.24552694X-RAY DIFFRACTION99.86
1.44-1.460.28271400.23372664X-RAY DIFFRACTION99.86
1.46-1.490.28651400.20822664X-RAY DIFFRACTION99.96
1.49-1.510.23471410.19522676X-RAY DIFFRACTION99.96
1.51-1.540.22151410.19672673X-RAY DIFFRACTION99.93
1.54-1.560.24011420.18462699X-RAY DIFFRACTION99.96
1.56-1.590.21921420.16612692X-RAY DIFFRACTION99.86
1.59-1.630.1991390.16232641X-RAY DIFFRACTION100
1.63-1.660.21641410.16152681X-RAY DIFFRACTION99.96
1.66-1.70.1861420.15582693X-RAY DIFFRACTION99.96
1.7-1.740.19351410.15842687X-RAY DIFFRACTION99.89
1.74-1.790.19841410.1552677X-RAY DIFFRACTION99.93
1.79-1.840.18251410.14152670X-RAY DIFFRACTION99.93
1.84-1.90.19281420.14142695X-RAY DIFFRACTION100
1.9-1.970.19971410.1482691X-RAY DIFFRACTION99.89
1.97-2.050.16271410.14632678X-RAY DIFFRACTION99.96
2.05-2.140.17841420.14462693X-RAY DIFFRACTION100
2.14-2.260.19031410.14462677X-RAY DIFFRACTION99.93
2.26-2.40.17731420.14752690X-RAY DIFFRACTION99.89
2.4-2.580.17771430.15162720X-RAY DIFFRACTION99.93
2.58-2.840.18091410.15532684X-RAY DIFFRACTION99.96
2.84-3.250.15721430.15442720X-RAY DIFFRACTION99.86
3.25-4.10.15491430.13592709X-RAY DIFFRACTION99.89
4.1-46.750.13241460.13582768X-RAY DIFFRACTION99.97

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