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

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Basic information

Entry
Database: PDB / ID: 4qrb
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 / peptide cross linkage / peptidoglycan stems / Bacterial cell wall periplasmic region
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-MLD / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)38,6012
Polymers37,6791
Non-polymers9221
Water3,765209
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)77,2014
Polymers75,3582
Non-polymers1,8442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3130 Å2
ΔGint-14 kcal/mol
Surface area30830 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-674-

HOH

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Components

#1: Protein 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 4.6
Details: 0.02 M calcium chloride, 0.1 M sodium acetate buffer (pH 4.6 to 5), and 30% methyl-2,4-pentanediol (v/v), 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: Apr 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.64→42.52 Å / Num. obs: 48214 / % possible obs: 99 % / Rmerge(I) obs: 0.0303 / Net I/σ(I): 19.85

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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 / Resolution: 1.64→42.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.975 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23605 2431 5 %RANDOM
Rwork0.21431 ---
obs0.21543 45715 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.1 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.64→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 49 209 2812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192718
X-RAY DIFFRACTIONr_bond_other_d0.0010.022501
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.9273722
X-RAY DIFFRACTIONr_angle_other_deg0.99135736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20524.153118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1611516
X-RAY DIFFRACTIONr_chiral_restr0.140.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02629
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: 1.643→1.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 157 -
Rwork0.272 2959 -
obs--87.11 %
Refinement TLS params.Method: refined / Origin x: 12.265 Å / Origin y: 17.3681 Å / Origin z: 84.0296 Å
111213212223313233
T0.0775 Å2-0.0409 Å20.0472 Å2-0.0788 Å2-0.0377 Å2--0.034 Å2
L0.1664 °2-0.0303 °20.3165 °2-0.6018 °20.2276 °2--1.1887 °2
S-0.0031 Å °0.0483 Å °-0.0212 Å °-0.1826 Å °0.0891 Å °-0.1233 Å °-0.0264 Å °0.1224 Å °-0.086 Å °

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