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- PDB-7ago: crystal structure of the N-acetylmuramyl-L-alanine amidase, Ami1,... -

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Basic information

Entry
Database: PDB / ID: 7ago
Titlecrystal structure of the N-acetylmuramyl-L-alanine amidase, Ami1, from Mycobacterium abscessus bound to L-Alanine-D-isoglutamine
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsSUGAR BINDING PROTEIN / amidase / peptidoglycan
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
: / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase
Similarity search - Domain/homology
ALANINE / D-alpha-glutamine / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBlaise, M.
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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,2524
Polymers23,9521
Non-polymers3013
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.740, 85.740, 75.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-511-

HOH

31A-616-

HOH

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Components

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


Mass: 23951.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E76_07740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A418LHZ8
#2: Chemical ChemComp-ZGL / D-alpha-glutamine / Iso-D-glutamine


Type: D-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 1.6 M ammonium sulfate, 1% (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: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31543 / % possible obs: 99.8 % / Redundancy: 26.1 % / Biso Wilson estimate: 20.97 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.12 / Net I/σ(I): 3.7
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 8799 / CC1/2: 0.93 / Rrim(I) all: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
PHENIX1.15rc3_3435refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AGL

7agl


Resolution: 1.7→47.3 Å / SU ML: 0.1864 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1869 2000 6.34 %
Rwork0.1624 29538 -
obs0.1639 31538 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 16 242 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551659
X-RAY DIFFRACTIONf_angle_d0.76852257
X-RAY DIFFRACTIONf_chiral_restr0.0482250
X-RAY DIFFRACTIONf_plane_restr0.0053308
X-RAY DIFFRACTIONf_dihedral_angle_d10.773998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31191400.26792081X-RAY DIFFRACTION100
1.74-1.790.2551410.23032076X-RAY DIFFRACTION99.95
1.79-1.840.24991400.2022067X-RAY DIFFRACTION100
1.84-1.90.23261410.2022080X-RAY DIFFRACTION99.82
1.9-1.970.26571400.19652062X-RAY DIFFRACTION99.59
1.97-2.050.17291420.15032096X-RAY DIFFRACTION99.96
2.05-2.140.19381410.14612081X-RAY DIFFRACTION99.96
2.14-2.250.19731400.15682083X-RAY DIFFRACTION98.93
2.25-2.40.1971420.15742083X-RAY DIFFRACTION99.11
2.4-2.580.171430.15072109X-RAY DIFFRACTION100
2.58-2.840.17121430.1542119X-RAY DIFFRACTION99.96
2.84-3.250.18421450.16692141X-RAY DIFFRACTION99.96
3.25-4.10.15211470.14962164X-RAY DIFFRACTION99.78
4.1-47.30.17751550.1542296X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6495164912040.5611421678210.4326797002882.59586433738-1.139918613561.54146969493-0.05206884315-0.00640484488365-0.1042014227650.000970419007459-0.0317973342260.07105277535140.09120299083390.0796836842370.2144165544560.1224429329280.00616138479509-0.0255878581930.166147275459-0.01257249844670.131998506018-4.438368888422.386212649-15.436285124
20.3612246143261.157500838540.6945747384454.19449597262.505836774811.481627527780.0448299738823-0.0495425778523-0.01760534112860.162502334966-0.03979035622980.04525258924940.113246321234-0.0226610862006-0.1607657507530.212009781452-0.0023094281644-0.01293526348960.2206214436026.92607545565E-50.177096531355-1.8209142070819.733016986-6.33652905315
33.417024809250.279169197274-1.624940242471.22913919471-0.00480231876612.90034935218-0.0004632706903950.1784794670520.148606352542-0.07586626045240.0235616738253-0.0397350246739-0.144081588504-0.0745784812521-0.05753193983340.1449778877080.00546079532188-0.01798384849420.123497232250.007576894112610.128667164710.65500463868731.5662015764-18.4111550752
42.803590515963.09313110904-4.681289160766.44800527472-5.900048688478.22794892096-0.05176467926280.2196731679-0.0427571076839-0.09858718789330.1256243820060.1375810383910.257985964987-0.31314503559-0.009933204985190.159352647799-0.00206762369186-0.04357774131330.177410759195-0.02016192041310.154634832932-6.1698814028919.4236279966-21.7956299718
51.029424771670.1718865466020.5616903955551.145072606340.5848200446611.235059509330.01948193949690.121154314378-0.115346245012-0.005576075499840.0391488040495-0.07311329919930.02661794115110.0959658574711-0.0708810812650.1556641718390.008593372309230.0002206564209770.18324587304-0.006571580601490.1694560092310.289644838818.3615374741-14.3489438896
61.445660531121.29703639891.665727489954.88613914534.234420440117.87138867455-0.007940156167160.2392669396270.0017382881732-0.200888521880.220988330454-0.411983827324-0.2319042273050.403636855538-0.2955416210130.145523287452-0.02851662678150.01092552404360.2142164795830.02182361552440.16568202071513.640424732129.1453950515-20.4168634047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 205 )
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 227 )

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