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- PDB-3vyn: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 3vyn
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N55 truncation mutant (resideus 55-408)
ComponentsProbable conserved lipoprotein LPPS
KeywordsTRANSFERASE / BETA BARREL / YkuD domain / L / D-transpeptidase / beta-lactam binding
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3780 / 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 - #3780 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, W.J. / Li, D.F. / Bi, L.J. / Wang, D.C.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis
Authors: Li, W.J. / Li, D.F. / Hu, Y.L. / Zhang, X.E. / Bi, L.J. / Wang, D.C.
History
DepositionSep 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable conserved lipoprotein LPPS
B: Probable conserved lipoprotein LPPS


Theoretical massNumber of molelcules
Total (without water)76,1322
Polymers76,1322
Non-polymers00
Water5,477304
1
A: Probable conserved lipoprotein LPPS


Theoretical massNumber of molelcules
Total (without water)38,0661
Polymers38,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable conserved lipoprotein LPPS


Theoretical massNumber of molelcules
Total (without water)38,0661
Polymers38,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.100, 93.150, 75.500
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable conserved lipoprotein LPPS / L / D-transpeptidase


Mass: 38066.195 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, residue 55-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2518c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O53223, UniProt: I6Y9J2*PLUS, EC: 2.3.2.12
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bis-Tis, 200mM MgCl2, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96422 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96422 Å / Relative weight: 1
ReflectionResolution: 2.5→51.03 Å / Num. all: 29344 / Num. obs: 29308 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4207 / Rsym value: 0.497 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYO

3vyo


Resolution: 2.5→48.64 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1433 -RANDOM
Rwork0.2198 ---
obs0.2198 29291 99.8 %-
all-29344 --
Displacement parametersBiso mean: 27.25 Å2
Baniso -1Baniso -2Baniso -3
1-6.657 Å20 Å2-1.593 Å2
2--4.16 Å20 Å2
3----10.817 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 0 0 304 5555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.3483 124 -
Rwork0.309 --
obs-2771 99.2 %

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