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- PDB-3tx4: Crystal Structure of Mutant (C354A) M. tuberculosis LD-transpepti... -

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Basic information

Entry
Database: PDB / ID: 3tx4
TitleCrystal Structure of Mutant (C354A) M. tuberculosis LD-transpeptidase type 2
ComponentsMycobacterium 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
L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsErdemli, S. / Bianchet, M.A. / 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 22, 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycobacterium Tuberculosis LD-transpeptidase type 2
B: Mycobacterium Tuberculosis LD-transpeptidase type 2


Theoretical massNumber of molelcules
Total (without water)62,1912
Polymers62,1912
Non-polymers00
Water5,296294
1
A: Mycobacterium Tuberculosis LD-transpeptidase type 2


Theoretical massNumber of molelcules
Total (without water)31,0951
Polymers31,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycobacterium Tuberculosis LD-transpeptidase type 2


Theoretical massNumber of molelcules
Total (without water)31,0951
Polymers31,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.784, 121.031, 122.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Mycobacterium Tuberculosis LD-transpeptidase type 2


Mass: 31095.473 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.54 Å3/Da / Density % sol: 65.29 %
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, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: 2009
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 38433 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.097 / Χ2: 1.098 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.32-2.364.30.49818550.733197.5
2.36-2.45.20.50318650.724199.1
2.4-2.456.10.46119050.765199.7
2.45-2.57.10.419060.802199.9
2.5-2.557.20.36419050.8211100
2.55-2.617.30.35419090.8271100
2.61-2.687.40.3319120.91100
2.68-2.757.30.28419220.8591100
2.75-2.837.40.23619020.8691100
2.83-2.927.40.18818900.9851100
2.92-3.037.40.15719170.9881100
3.03-3.157.40.13219261.121100
3.15-3.297.40.10419241.0811100
3.29-3.477.40.08819261.2491100
3.47-3.687.40.07419201.1411100
3.68-3.977.40.06319401.2321100
3.97-4.377.40.05219481.1841100
4.37-57.40.04819501.2641100
5-6.297.30.05619741.411100
6.29-5070.06120372.589198.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→28.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 5.913 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1958 5.1 %RANDOM
Rwork0.2105 ---
obs0.2134 38418 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 29.8034 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---1.24 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.32→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 0 294 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214240
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9165805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60224.41195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55815613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3561521
X-RAY DIFFRACTIONr_chiral_restr0.1390.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213331
X-RAY DIFFRACTIONr_mcbond_it1.1381.52661
X-RAY DIFFRACTIONr_mcangle_it2.08524308
X-RAY DIFFRACTIONr_scbond_it3.53631579
X-RAY DIFFRACTIONr_scangle_it5.5724.51494
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 137 -
Rwork0.275 2580 -
all-2717 -
obs--96.93 %

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