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- PDB-7agl: crystal structure of the apo form of the N-acetylmuramyl-L-alanin... -

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Basic information

Entry
Database: PDB / ID: 7agl
Titlecrystal structure of the apo form of the N-acetylmuramyl-L-alanine amidase, Ami1, from Mycobacterium abscessus.
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 activity / peptidoglycan catabolic process / metal ion binding / N-acetylmuramoyl-L-alanine amidase
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)24,0172
Polymers23,9521
Non-polymers651
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.920, 85.920, 73.660
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-424-

HOH

21A-525-

HOH

31A-594-

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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 1.6 M ammonium sulfate and, 1% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→60.7 Å / Num. obs: 35745 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 10.45
Reflection shellResolution: 1.6→1.65 Å / Num. unique obs: 5957 / CC1/2: 0.53 / Rrim(I) all: 1.13

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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: 4LQ6

4lq6


Resolution: 1.6→38.42 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 2000 5.6 %
Rwork0.1682 33743 -
obs0.1698 35743 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 1 232 1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681630
X-RAY DIFFRACTIONf_angle_d0.88542218
X-RAY DIFFRACTIONf_chiral_restr0.0518245
X-RAY DIFFRACTIONf_plane_restr0.0061302
X-RAY DIFFRACTIONf_dihedral_angle_d10.5253980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33131440.30252423X-RAY DIFFRACTION99.07
1.64-1.680.2811430.26252423X-RAY DIFFRACTION99
1.68-1.730.28221420.25922395X-RAY DIFFRACTION98.72
1.73-1.790.24631430.23142410X-RAY DIFFRACTION97.59
1.79-1.850.22361430.20552401X-RAY DIFFRACTION97.28
1.85-1.930.23771420.17652399X-RAY DIFFRACTION98.18
1.93-2.020.19731430.16512423X-RAY DIFFRACTION98.28
2.02-2.120.18431430.15992417X-RAY DIFFRACTION97.52
2.12-2.250.19951430.15352408X-RAY DIFFRACTION97.29
2.25-2.430.19661420.15552398X-RAY DIFFRACTION96.54
2.43-2.670.18971390.1652348X-RAY DIFFRACTION93.64
2.67-3.060.18541440.17912417X-RAY DIFFRACTION95.88
3.06-3.850.19671430.15552419X-RAY DIFFRACTION94.85
3.85-38.420.16441460.14542462X-RAY DIFFRACTION91.35
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)
11.368347432670.3175635621330.7600622963862.077097783580.5910126656960.8891230680380.0305380337718-0.0842852404348-0.08353676068990.162053633191-0.03244758560620.07776299928250.0851263658047-0.03238489522420.018036673390.1891898172920.01227466470510.006171205128050.2340644395950.01562202314960.19012906457-3.1262836645321.1723420311-11.2474804524
22.75844180916-0.738054340578-0.6130975952141.77662851410.7032283915825.6099139630.02947934954520.2230538484610.276430227765-0.09916994647660.0843686709716-0.105020104341-0.514050897414-0.0111333435467-0.07254708319830.220455757859-0.0212882392138-0.01649779804350.2145180318020.01390875852570.2056944381554.3168295896133.1698060223-17.9713935635
31.51421041316-0.08319546342290.6656361680021.386120225970.1264820311981.287264363880.0266551978180.208044015099-0.173348891223-0.04861694154490.0352924880509-0.1551011243740.06519828061370.0947394871619-0.09109130225990.191749010299-0.004177738498350.01021645982280.224649366872-0.02066274941270.218649614336.0973749954618.8234627111-17.0734722428
41.613929827030.4196903168720.8087069564142.703679589691.051906633274.23038662127-0.09682017256190.18527901785-0.00926844671113-0.09414172897310.131848939631-0.216450983542-0.4012159509630.191612751688-0.0145080355110.172160264902-0.0154887156699-0.00129399803120.226867658380.002279223954530.22636542643612.897583371429.7867202852-13.2272090263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 226 )

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