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- PDB-4qr7: Structure and specificity of L-D-Transpeptidase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4qr7
TitleStructure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
ComponentsL,d-transpeptidase LdtB
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / L-D-transpeptidase / D-D-transpeptidase / Single anomalous diffraction / imipenem / meropenem / peptidoglycan / beta-lactamase
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-DWZ / Chem-MLD / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.303 Å
AuthorsGokulan, K. / Varughese, K.I.
CitationJournal: To be Published
Title: Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
Authors: Gokulan, K. / Khare, S. / Cerniglia, C.E. / Foley, S.L. / Varughese, K.I.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L,d-transpeptidase LdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9863
Polymers37,6791
Non-polymers1,3072
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L,d-transpeptidase LdtB
hetero molecules

A: L,d-transpeptidase LdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9726
Polymers75,3582
Non-polymers2,6154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area3200 Å2
ΔGint-17 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.330, 66.459, 206.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein L,d-transpeptidase LdtB / Probable L / D-transpeptidase LdtB


Mass: 37678.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ldtB, Rv2518c, RVBD_2518c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: I6Y9J2
#2: Chemical ChemComp-MLD / GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA / 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE


Mass: 921.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H59N7O20
#3: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium malonate (pH 7.0) and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→103.4 Å / Rmerge(I) obs: 0.0556 / Net I/σ(I): 13.98

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.303→33.249 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 814 5 %
Rwork0.2028 --
obs0.2059 16293 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→33.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 80 80 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082700
X-RAY DIFFRACTIONf_angle_d1.1793697
X-RAY DIFFRACTIONf_dihedral_angle_d12.874941
X-RAY DIFFRACTIONf_chiral_restr0.077414
X-RAY DIFFRACTIONf_plane_restr0.005486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3027-2.44690.33681390.24162309X-RAY DIFFRACTION84
2.4469-2.63580.30541260.24382489X-RAY DIFFRACTION89
2.6358-2.90090.30971410.23872549X-RAY DIFFRACTION91
2.9009-3.32030.28881110.23022631X-RAY DIFFRACTION92
3.3203-4.18190.26221600.18812697X-RAY DIFFRACTION95
4.1819-33.25280.21131370.16722804X-RAY DIFFRACTION94

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