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- PDB-6d5a: Crystal structure of L,D-transpeptidase 5 from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 6d5a
TitleCrystal structure of L,D-transpeptidase 5 from Mycobacterium tuberculosis in apo form
ComponentsL,D-transpeptidase 5
KeywordsTRANSFERASE / L / D transpeptidation / apo form
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
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 catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel ...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 catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
L,D-transpeptidase 5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.622 Å
AuthorsLibreros, G.A. / Dias, M.V.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
CitationJournal: ACS Infect Dis / Year: 2019
Title: Structural Basis for the Interaction and Processing of beta-Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis.
Authors: Libreros-Zuniga, G.A. / Dos Santos Silva, C. / Salgado Ferreira, R. / Dias, M.V.B.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Assembly

Deposited unit
A: L,D-transpeptidase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0572
Polymers41,8621
Non-polymers1941
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.446, 97.446, 193.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

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Components

#1: Protein L,D-transpeptidase 5 / LDT 5 / Ldt(Mt5)


Mass: 41862.469 Da / Num. of mol.: 1 / Fragment: residues 50-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: lprQ, Rv0483, MTCY20G9.09 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WKV3, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.4 Å3/Da / Density % sol: 63.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000 22% (w/v), sodium acetate 100 mM, ammonium sulphate 200 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.62→43.54 Å / Num. obs: 15940 / % possible obs: 94.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 60.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.048 / Rrim(I) all: 0.126 / Net I/σ(I): 9.7 / Num. measured all: 85436 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.62-2.745.30.89618780.7410.380.98393.8
9.08-43.544.40.0414400.9930.020.04686.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DU7

5du7


Resolution: 2.622→43.538 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.2608 785 4.94 %
Rwork0.2059 --
obs0.2087 15879 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.68 Å2 / Biso mean: 72.6603 Å2 / Biso min: 32.35 Å2
Refinement stepCycle: final / Resolution: 2.622→43.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 13 87 2711
Biso mean--103.64 61.17 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012705
X-RAY DIFFRACTIONf_angle_d1.1543706
X-RAY DIFFRACTIONf_chiral_restr0.059408
X-RAY DIFFRACTIONf_plane_restr0.013486
X-RAY DIFFRACTIONf_dihedral_angle_d18.2781570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6223-2.78650.42421360.35582427256393
2.7865-3.00160.33991330.29482482261595
3.0016-3.30360.29241270.24742504263194
3.3036-3.78140.29631140.20572535264994
3.7814-4.76320.25721380.16392526266493
4.7632-43.54380.19341370.17922620275790
Refinement TLS params.Method: refined / Origin x: -80.783 Å / Origin y: 87.0816 Å / Origin z: 31.0168 Å
111213212223313233
T0.5389 Å20.0959 Å20.0535 Å2-0.3395 Å20.0095 Å2--0.4598 Å2
L0.637 °20.1042 °2-0.3331 °2-0.2848 °2-0.233 °2--1.5544 °2
S-0.0989 Å °-0.0324 Å °-0.0773 Å °-0.1376 Å °0.0495 Å °-0.2793 Å °-0.1087 Å °0.0849 Å °0.0471 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA55 - 416
2X-RAY DIFFRACTION1allS4 - 80
3X-RAY DIFFRACTION1allS81 - 98
4X-RAY DIFFRACTION1allB1

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