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

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Basic information

Entry
Database: PDB / ID: 4qra
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
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
L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,3983
Polymers75,3582
Non-polymers401
Water5,350297
1
A: L,d-transpeptidase LdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7192
Polymers37,6791
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,d-transpeptidase LdtB


Theoretical massNumber of molelcules
Total (without water)37,6791
Polymers37,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.758, 88.132, 90.512
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L,d-transpeptidase LdtB


Mass: 37678.844 Da / Num. of mol.: 2
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
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: 2.29→34.86 Å / Num. obs: 37534 / % possible obs: 96.4 % / Rmerge(I) obs: 0.0572 / Net I/σ(I): 16.21

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→34.86 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.388 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1964 5 %RANDOM
Rwork0.18181 ---
obs0.18409 37354 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-0.28 Å2
2---1.57 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.29→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 1 297 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195187
X-RAY DIFFRACTIONr_bond_other_d0.0010.024735
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9227100
X-RAY DIFFRACTIONr_angle_other_deg0.931310860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0335663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91424.138232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3011531
X-RAY DIFFRACTIONr_chiral_restr0.1260.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
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: 2.291→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 139 -
Rwork0.207 2656 -
obs--94.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2428-0.1994-0.06931.1037-0.19840.28180.0095-0.0694-0.0112-0.1188-0.03050.0540.10180.01460.0210.0435-0.0020.01010.0349-0.00010.0216-39.8928-3.1446-36.9757
20.21190.07690.07781.1251-0.1750.27360.00570.0787-0.00010.0992-0.03180.0281-0.09610.01180.02610.040.0083-0.00620.0388-0.00020.0195-39.9036-29.6968-8.3427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 408
2X-RAY DIFFRACTION2B65 - 408
3X-RAY DIFFRACTION2A501

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