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

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Basic information

Entry
Database: PDB / ID: 6iyw
TitleCrystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with Imipenem 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 / extracellular region / 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-IM2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, D.F. / Zhao, F. / Wang, D.C.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: The 1-beta-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2 for 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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
C: L,D-transpeptidase 2
D: L,D-transpeptidase 2
E: L,D-transpeptidase 2
F: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,33536
Polymers177,3166
Non-polymers4,01830
Water29,5811642
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3157
Polymers29,5531
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4078
Polymers29,5531
Non-polymers8547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0384
Polymers29,5531
Non-polymers4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9463
Polymers29,5531
Non-polymers3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4078
Polymers29,5531
Non-polymers8547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2226
Polymers29,5531
Non-polymers6705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.200, 103.696, 103.809
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29552.693 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1642 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NaCl, HEPES, pH 6.5, PEG 3350

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 201419 / % possible obs: 98.8 % / Redundancy: 6.78 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.084 / Net I/σ(I): 12.54
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 7.02 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 14762 / CC1/2: 0.891 / % possible all: 98.1

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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: 1.6→46.414 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1988 0.99 %Random
Rwork0.1863 ---
obs0.1867 201373 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→46.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12222 0 264 1642 14128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712866
X-RAY DIFFRACTIONf_angle_d1.1317545
X-RAY DIFFRACTIONf_dihedral_angle_d8.2999965
X-RAY DIFFRACTIONf_chiral_restr0.0861885
X-RAY DIFFRACTIONf_plane_restr0.0072290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27941450.265714034X-RAY DIFFRACTION98
1.64-1.68440.25971430.242314126X-RAY DIFFRACTION98
1.6844-1.73390.27631480.22514164X-RAY DIFFRACTION98
1.7339-1.78990.29491420.218114203X-RAY DIFFRACTION98
1.7899-1.85390.23771410.211514158X-RAY DIFFRACTION99
1.8539-1.92810.24841400.198614216X-RAY DIFFRACTION99
1.9281-2.01580.24451460.196914194X-RAY DIFFRACTION99
2.0158-2.12210.25351350.188414239X-RAY DIFFRACTION99
2.1221-2.25510.23141490.18914276X-RAY DIFFRACTION99
2.2551-2.42920.22831380.19314288X-RAY DIFFRACTION99
2.4292-2.67360.2321390.194214355X-RAY DIFFRACTION99
2.6736-3.06040.22551460.186414311X-RAY DIFFRACTION99
3.0604-3.85550.19541370.166614466X-RAY DIFFRACTION100
3.8555-46.43380.18651390.164114355X-RAY DIFFRACTION98

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