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- PDB-9cun: Crystal structure of Ami1 from M. tuberculosis in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 9cun
TitleCrystal structure of Ami1 from M. tuberculosis in complex with a tetrazole compound
ComponentsN-acetylmuramoyl-L-alanine amidase Rv3717
KeywordsHYDROLASE / amidase / peptidoglycan hydrolase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / FtsZ-dependent cytokinesis / peptidoglycan catabolic process / cell wall organization / cell wall macromolecule catabolic process / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
: / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase
Similarity search - Domain/homology
: / N-acetylmuramoyl-L-alanine amidase Rv3717
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMartinez-Caballero, S.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IA205122 Mexico
CitationJournal: Acs Omega / Year: 2024
Title: Identification of Potential Inhibitors of Mycobacterium tuberculosis Amidases: An Integrated In Silico and Experimental Study.
Authors: Rosas-Cruz, M. / Madariaga Mazon, A. / Garcia-Mejia, C.D. / Hernandez-Vazquez, E. / Gomez-Velasco, H. / Jimenez-Faraco, E. / Farias-Gaytan, R.S. / Hermoso, J.A. / Martinez-Caballero, S.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase Rv3717
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0343
Polymers22,6961
Non-polymers3372
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.353, 103.960, 130.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase Rv3717 / Zinc-dependent peptidoglycan amidase


Mass: 22696.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3717 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6Y4D2, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-A1A0I / 5-(2-iodophenyl)-2H-tetrazole


Mass: 272.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5IN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium sulphate Sodium chloride HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→40.04 Å / Num. obs: 44854 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 2182 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→40.04 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 2267 5.05 %
Rwork0.1798 42582 -
obs0.1808 44849 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.81 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 13 160 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621625
X-RAY DIFFRACTIONf_angle_d0.8872210
X-RAY DIFFRACTIONf_chiral_restr0.0734238
X-RAY DIFFRACTIONf_plane_restr0.0105305
X-RAY DIFFRACTIONf_dihedral_angle_d6.9555241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.25831220.20322603X-RAY DIFFRACTION97.88
1.48-1.520.21481640.18892599X-RAY DIFFRACTION98.19
1.52-1.550.21311440.18352616X-RAY DIFFRACTION97.8
1.55-1.60.19971580.17942592X-RAY DIFFRACTION98.6
1.6-1.640.19971130.17692669X-RAY DIFFRACTION98.51
1.64-1.70.2411420.18752640X-RAY DIFFRACTION98.86
1.7-1.760.22911290.18882642X-RAY DIFFRACTION98.54
1.76-1.830.21541580.17612628X-RAY DIFFRACTION99
1.83-1.910.19071200.17562662X-RAY DIFFRACTION98.76
1.91-2.010.18351410.16572672X-RAY DIFFRACTION99.29
2.01-2.140.17891460.16992687X-RAY DIFFRACTION99.4
2.14-2.30.14971470.16182670X-RAY DIFFRACTION99.37
2.3-2.530.17421470.1792690X-RAY DIFFRACTION99.33
2.53-2.90.22031440.19892706X-RAY DIFFRACTION98.96
2.9-3.650.20531500.19282700X-RAY DIFFRACTION98.17
3.65-40.040.21241420.17012806X-RAY DIFFRACTION96.66

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