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- PDB-7kem: Crystallographic structure of L,D-transpeptidase 2 from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 7kem
TitleCrystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / Transpeptidase / Peptidoglycan synthesis
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 / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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.
Similarity search - Domain/homology
Di-mu-iodobis(ethylenediamine)diplatinum(II) / 6-CARBOXYLYSINE / D-GLUTAMIC ACID / : / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLibreros, G.A. / Dias, M.V.B.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia2010/15971-3 Portugal
CitationJournal: To Be Published
Title: Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis.
Authors: Libreros, G.A. / Dias, M.V.B.
History
DepositionOct 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country

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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)93,46213
Polymers86,8152
Non-polymers6,64711
Water00
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6116
Polymers43,4081
Non-polymers3,2045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8517
Polymers43,4081
Non-polymers3,4436
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.528, 121.051, 122.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 43407.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical
ChemComp-0JC / Di-mu-iodobis(ethylenediamine)diplatinum(II)


Mass: 764.162 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H16I2N4Pt2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-6CL / 6-CARBOXYLYSINE


Type: L-peptide linking / Mass: 191.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N2O4
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 3M NaOAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.77→49.66 Å / Num. obs: 80670 / % possible obs: 99.6 % / Redundancy: 12.3 % / Biso Wilson estimate: 22.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Net I/σ(I): 15.6
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8453 / CC1/2: 0.824 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUR

3tur


Resolution: 1.77→49.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.876 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 4212 5 %RANDOM
Rwork0.2612 ---
obs0.2619 80670 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.58 Å2 / Biso mean: 25.543 Å2 / Biso min: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.77→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 0 0 4039
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124188
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6325735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.92422.944214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5911521
X-RAY DIFFRACTIONr_chiral_restr0.1110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023299
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 306 -
Rwork0.309 5908 -
all-6214 -
obs--99.97 %

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