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

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Basic information

Entry
Database: PDB / ID: 4qtf
TitleStructure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
ComponentsL,d-transpeptidase LdtB
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Structural Genomics / Enzyme Function Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / L-D-transpeptidase / D-D-transpeptidase / imipenem / meropenem / peptidoglycan / beta-lactamase / cross-linkage / HYDROLASE-HYDROLASE INHIBITOR complex
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 ...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-3V5 / Chem-MLD / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)38,5933
Polymers37,3811
Non-polymers1,2112
Water1,36976
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)77,1856
Polymers74,7632
Non-polymers2,4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3150 Å2
ΔGint-14 kcal/mol
Surface area31670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.272, 65.881, 207.456
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-626-

HOH

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Components

#1: Protein L,d-transpeptidase LdtB


Mass: 37381.453 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-3V5 / (3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline / olivanic acid analog, open from


Mass: 289.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.03 M citric acid, 0.07 M BIS-TRIS propane pH 7.6 and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
PH range: 7,6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MAR-325 CCD detector / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.3 Å / Num. obs: 25603

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QR7

4qr7


Resolution: 2→42.35 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.918 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25766 1356 5 %RANDOM
Rwork0.21298 ---
obs0.21522 25603 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.38 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 65 76 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192786
X-RAY DIFFRACTIONr_bond_other_d0.0010.022568
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.9553812
X-RAY DIFFRACTIONr_angle_other_deg0.95535891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38524.153118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0051516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 94 -
Rwork0.245 1863 -
obs--99.49 %
Refinement TLS params.Method: refined / Origin x: 12.5731 Å / Origin y: 15.7551 Å / Origin z: 19.5679 Å
111213212223313233
T0.058 Å20.0325 Å2-0.043 Å2-0.0284 Å2-0.0429 Å2--0.0923 Å2
L0.0795 °20.0181 °2-0.0253 °2-0.5535 °20.3102 °2--1.4056 °2
S-0.0185 Å °-0.0243 Å °0.0257 Å °0.1523 Å °0.0895 Å °-0.1039 Å °0.0034 Å °0.0836 Å °-0.071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 407
2X-RAY DIFFRACTION1A501

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