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- PDB-6iyv: Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6iyv
TitleCrystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ertapenem adduct
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / LD-TRANSPEPTIDASE / PEPTIDOGLYCAN SYNTHESIS ENZYME / beta-lactam binding
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 / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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
Chem-2RG / DI(HYDROXYETHYL)ETHER / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhao, F. / Li, D.F. / Wang, D.C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: The 1-beta-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2for ertapenem than for imipenem.
Authors: Zhao, F. / Hou, Y.J. / Zhang, Y. / Wang, D.C. / Li, D.F.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
B: L,D-transpeptidase 2
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,41218
Polymers59,1052
Non-polymers2,30616
Water12,394688
1
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,79910
Polymers29,5531
Non-polymers1,2469
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6138
Polymers29,5531
Non-polymers1,0607
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.365, 73.188, 104.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 29552.693 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: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 6 types, 704 molecules

#2: Chemical ChemComp-2RG / (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ERTAPENEM, bound form POST-ISOMERIZED / Ertapenem


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O7S / Comment: medication, antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: NaCl, Bis-Tris, pH 6.0, PEG 3350

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 84210 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.073 / Net I/σ(I): 26.92
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 3.42 / Num. unique obs: 6190 / CC1/2: 0.931 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYP

3vyp


Resolution: 1.5→45.052 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.37
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 1999 2.37 %Random
Rwork0.174 ---
obs0.1743 84189 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→45.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 153 688 4921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054349
X-RAY DIFFRACTIONf_angle_d0.8875930
X-RAY DIFFRACTIONf_dihedral_angle_d13.1732453
X-RAY DIFFRACTIONf_chiral_restr0.061640
X-RAY DIFFRACTIONf_plane_restr0.006763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.26271390.23995825X-RAY DIFFRACTION100
1.5375-1.57910.21011450.20575780X-RAY DIFFRACTION100
1.5791-1.62560.20081310.18925837X-RAY DIFFRACTION100
1.6256-1.6780.21951520.18685786X-RAY DIFFRACTION100
1.678-1.7380.21021330.18495833X-RAY DIFFRACTION100
1.738-1.80760.21391490.17815827X-RAY DIFFRACTION100
1.8076-1.88990.18511390.17755835X-RAY DIFFRACTION100
1.8899-1.98950.20651450.17535832X-RAY DIFFRACTION100
1.9895-2.11410.20921350.17165864X-RAY DIFFRACTION100
2.1141-2.27740.16221530.17175871X-RAY DIFFRACTION100
2.2774-2.50650.20221410.17535880X-RAY DIFFRACTION100
2.5065-2.86920.2071400.1815927X-RAY DIFFRACTION100
2.8692-3.61460.1721520.16325937X-RAY DIFFRACTION99
3.6146-45.07210.15661450.16036156X-RAY DIFFRACTION99

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