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- PDB-5lb1: Crystal structure of the Mycobacterium tuberculosis L,D-transpept... -

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Basic information

Entry
Database: PDB / ID: 5lb1
TitleCrystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with thionitrobenzoate (TNB) adduct at the active site cysteine-354
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / cell wall / peptidoglycan / transpeptidase / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / : / 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 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / : / 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. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-MERCAPTO-2-NITRO-BENZOIC ACID / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSteiner, E.M. / Schnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Research Council Sweden
CitationJournal: FEBS J. / Year: 2017
Title: Binding and processing of beta-lactam antibiotics by the transpeptidase LdtMt2 from Mycobacterium tuberculosis.
Authors: Steiner, E.M. / Schneider, G. / Schnell, R.
History
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jan 10, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4164
Polymers57,0172
Non-polymers3982
Water12,106672
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7082
Polymers28,5091
Non-polymers1991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7082
Polymers28,5091
Non-polymers1991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.368, 53.910, 57.174
Angle α, β, γ (deg.)68.84, 75.03, 88.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 28508.646 Da / Num. of mol.: 2 / Fragment: UNP residues 149-408
Source method: isolated from a genetically manipulated source
Details: Covalent adduct (Thio-nitro-benzoate) on Cys354, mixed disulphide bond
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pNIC28Bsa4 / Details (production host): N-terminal His-tag / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: spear tip
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES/Imidazol pH 6.5 0.02M of each carboxylic acid (sodium formate, ammonium acetate, tri-sodium citrate, sodium potassium DL-tartrate, sodium oxamate) 10% PEG 20000 20%PEGMME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2014 / Details: Pt coated mirrors
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.55→51.4 Å / Num. obs: 79462 / % possible obs: 95.3 % / Observed criterion σ(I): 1.7 / Redundancy: 2 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/av σ(I): 9.7 / Net I/σ(I): 9.7
Reflection shellResolution: 1.55→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.7 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUC

4huc


Resolution: 1.55→51.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.013 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19415 3953 5 %RANDOM
Rwork0.14746 ---
obs0.14981 75507 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20.12 Å2-0.03 Å2
2---0.06 Å2-0.12 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.55→51.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 26 672 4633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194247
X-RAY DIFFRACTIONr_bond_other_d0.0010.023835
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9215836
X-RAY DIFFRACTIONr_angle_other_deg0.87938815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65424.072194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8215621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1771524
X-RAY DIFFRACTIONr_chiral_restr0.090.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021019
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.27938082
X-RAY DIFFRACTIONr_sphericity_free29.8135190
X-RAY DIFFRACTIONr_sphericity_bonded8.5858434
LS refinement shellResolution: 1.549→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 255 -
Rwork0.267 5388 -
obs--91 %

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