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- PDB-3tur: Crystal Structure of M. tuberculosis LD-transpeptidase type 2 com... -

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Basic information

Entry
Database: PDB / ID: 3tur
TitleCrystal Structure of M. tuberculosis LD-transpeptidase type 2 complexed with a peptidoglycan fragment
ComponentsMycobacteria Tuberculosis LD-transpeptidase type 2
KeywordsPEPTIDOGLYCAN BINDING PROTEIN / protein-peptidoglycan complex
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / 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
Di-mu-iodobis(ethylenediamine)diplatinum(II) / 6-CARBOXYLYSINE / D-GLUTAMIC ACID / : / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.72 Å
AuthorsBianchet, M.A. / Erdemli, S.B. / Gupta, R. / Lamichhane, G. / Amzel, L.M.
CitationJournal: Structure / Year: 2012
Title: Targeting the Cell Wall of Mycobacterium tuberculosis: Structure and Mechanism of L,D-Transpeptidase 2.
Authors: Erdemli, S.B. / Gupta, R. / Bishai, W.R. / Lamichhane, G. / Amzel, L.M. / Bianchet, M.A.
History
DepositionSep 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: Mycobacteria Tuberculosis LD-transpeptidase type 2
B: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,90213
Polymers62,2552
Non-polymers6,64711
Water8,467470
1
A: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5237
Polymers31,1281
Non-polymers3,3956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3796
Polymers31,1281
Non-polymers3,2525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-26 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.132, 120.829, 122.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mycobacteria Tuberculosis LD-transpeptidase type 2


Mass: 31127.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lppS, MT2594, Rv2518c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O53223

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Non-polymers , 5 types, 481 molecules

#2: Chemical
ChemComp-0JC / Di-mu-iodobis(ethylenediamine)diplatinum(II)


Mass: 764.162 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H16I2N4Pt2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID / Glutamic acid


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-6CL / 6-CARBOXYLYSINE / Diaminopimelic acid


Type: L-peptide linking / Mass: 191.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N2O4
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.55 Å3/Da / Density % sol: 65.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→85.7 Å / Num. all: 89172 / Num. obs: 84134 / % possible obs: 94.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.051 / Net I/σ(I): 29.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementResolution: 1.72→85.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1879 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8294 / SU B: 2.089 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0945 / SU Rfree: 0.0984 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 4474 5 %RANDOM
Rwork0.1985 ---
all0.2004 ---
obs0.2004 -94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 146.5 Å2 / Biso mean: 38.9314 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.72→85.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 71 470 4580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0224308
X-RAY DIFFRACTIONr_angle_refined_deg2.5951.9565908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76124.615195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815.262611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4031521
X-RAY DIFFRACTIONr_chiral_restr0.2010.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213459
X-RAY DIFFRACTIONr_mcbond_it1.5661.52647
X-RAY DIFFRACTIONr_mcangle_it2.59324287
X-RAY DIFFRACTIONr_scbond_it5.52531661
X-RAY DIFFRACTIONr_scangle_it8.6574.51618
X-RAY DIFFRACTIONr_rigid_bond_restr17.036310
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 287 -
Rwork0.302 5447 -
all-5734 -
obs--83.67 %

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