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- PDB-5uwv: Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2 -

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Basic information

Entry
Database: PDB / ID: 5uwv
TitleCrystal structure of Mycobacterium abscessus L,D-transpeptidase 2
ComponentsL,D-TRANSPEPTIDASE 2
KeywordsTRANSFERASE / L / D-transpeptidase / Peptidoglycan synthesis enzyme / cell wall enzyme / LdtMab2 / Mycobacterium abscessus
Function / homology
Function and homology information


acyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain ...Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable conserved lipoprotein LppS
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsKumar, P. / Ginell, S.L. / Lamichhane, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP2OD008459 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Mycobacterium abscessus l,d-Transpeptidases Are Susceptible to Inactivation by Carbapenems and Cephalosporins but Not Penicillins.
Authors: Kumar, P. / Chauhan, V. / Silva, J.R.A. / Lameira, J. / d'Andrea, F.B. / Li, S.G. / Ginell, S.L. / Freundlich, J.S. / Alves, C.N. / Bailey, S. / Cohen, K.A. / Lamichhane, G.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Aug 14, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: L,D-TRANSPEPTIDASE 2
A: L,D-TRANSPEPTIDASE 2
D: L,D-TRANSPEPTIDASE 2
E: L,D-TRANSPEPTIDASE 2
C: L,D-TRANSPEPTIDASE 2
F: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)237,1326
Polymers237,1326
Non-polymers00
Water1,08160
1
B: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: L,D-TRANSPEPTIDASE 2


Theoretical massNumber of molelcules
Total (without water)39,5221
Polymers39,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.239, 130.937, 135.664
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L,D-TRANSPEPTIDASE 2


Mass: 39522.059 Da / Num. of mol.: 6 / Fragment: UNP residues 42-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_1530 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MMQ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 13% PEG 8000, 110 mM sodium citrate tribasic dihydrate
PH range: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.98→135.53 Å / Num. obs: 65870 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 56.54 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.02
Reflection shellResolution: 2.98→3.087 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 5838 / CC1/2: 0.78 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DU7

5du7


Resolution: 2.98→135.53 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 18.041 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.565 / ESU R Free: 0.409
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3083 4.7 %RANDOM
Rwork0.1974 ---
obs0.2008 62793 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.68 Å2 / Biso mean: 58.908 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.22 Å2
2---0.12 Å20 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.98→135.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15128 0 0 60 15188
Biso mean---30 -
Num. residues----2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215450
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214288
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.92721050
X-RAY DIFFRACTIONr_angle_other_deg1.011332796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08251994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51424.844673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13152343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8431582
X-RAY DIFFRACTIONr_chiral_restr0.0870.22353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117918
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023492
LS refinement shellResolution: 2.981→3.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 194 -
Rwork0.301 4020 -
all-4214 -
obs--84.48 %

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