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- PDB-5e51: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 5.0E+51
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 with Faropenem adduct
ComponentsL,D-transpeptidase 1
KeywordsTRANSFERASE / L / D-transpeptidase 1 / Peptidoglycan synthesis enzyme / cell wall enzyme / ldtMt1 / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / periplasmic space / extracellular region
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 / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like ...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 / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
(3R)-3-hydroxybutanal / L,D-transpeptidase 1 / L,D-transpeptidase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKumar, P. / Lamichhane, G. / Ginell, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2OD008459-01 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Non-classical transpeptidases yield insight into new antibacterials.
Authors: Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G.
History
DepositionOct 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Assembly

Deposited unit
A: L,D-transpeptidase 1
B: L,D-transpeptidase 1
C: L,D-transpeptidase 1
D: L,D-transpeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0446
Polymers95,8684
Non-polymers1762
Water2,072115
1
A: L,D-transpeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0552
Polymers23,9671
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L,D-transpeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0552
Polymers23,9671
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.379, 58.379, 257.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
L,D-transpeptidase 1 / LDT 1 / Ldt(Mt1)


Mass: 23966.965 Da / Num. of mol.: 4 / Fragment: UNP residues 32-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: ldtA, MT0125 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7DAG3, UniProt: O53638*PLUS, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-5KO / (3R)-3-hydroxybutanal / Faropenem adduct


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFaropenem upon beta-lactam ring opening and aceylation to enzyme undergoes a further cleavage with ...Faropenem upon beta-lactam ring opening and aceylation to enzyme undergoes a further cleavage with a small peace of drug (R2 group) remaining attached to the enzyme as Faropenem adduct (5KO) in the structure.

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG6000, Bicine / PH range: pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.25→19.878 Å / Num. obs: 81604 / % possible obs: 87.85 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JMN

4jmn


Resolution: 2.25→19.878 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3724 4.57 %5
Rwork0.2576 ---
obs0.2586 81530 87.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→19.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 12 115 5886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015930
X-RAY DIFFRACTIONf_angle_d1.5248129
X-RAY DIFFRACTIONf_dihedral_angle_d13.6211984
X-RAY DIFFRACTIONf_chiral_restr0.061949
X-RAY DIFFRACTIONf_plane_restr0.0091032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2543-2.29310.4818760.48431604X-RAY DIFFRACTION35
2.2931-2.33470.35271980.33424318X-RAY DIFFRACTION90
2.3347-2.37950.30211880.3184120X-RAY DIFFRACTION93
2.3795-2.4280.40422100.31334432X-RAY DIFFRACTION94
2.428-2.48070.35142100.30354256X-RAY DIFFRACTION94
2.4807-2.53820.32362140.3174410X-RAY DIFFRACTION94
2.5382-2.60160.37812060.28774208X-RAY DIFFRACTION94
2.6016-2.67170.4531260.39152694X-RAY DIFFRACTION58
2.6717-2.75010.46971480.37952806X-RAY DIFFRACTION61
2.7501-2.83860.30342020.28474358X-RAY DIFFRACTION95
2.8386-2.93970.26312300.25434446X-RAY DIFFRACTION94
2.9397-3.0570.23471940.25024390X-RAY DIFFRACTION95
3.057-3.19550.23941980.24274332X-RAY DIFFRACTION95
3.1955-3.36310.29312060.24954380X-RAY DIFFRACTION95
3.3631-3.57250.32181600.29713060X-RAY DIFFRACTION66
3.5725-3.84630.38291600.26763220X-RAY DIFFRACTION69
3.8463-4.22950.34141680.2373506X-RAY DIFFRACTION76
4.2295-4.83280.1822120.16484462X-RAY DIFFRACTION95
4.8328-6.05620.18612100.19624312X-RAY DIFFRACTION95
6.0562-19.05720.25342080.21224432X-RAY DIFFRACTION95

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