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- PDB-5e1i: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 5e1i
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / Peptidoglycan synthesis enzyme / cell wall enzyme
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
Chem-6B8 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsKumar, P. / Ginell, S.L. / Lamichhane, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2OD008459-01 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Non-classical transpeptidases yield insight into new antibacterials.
Authors: Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4385
Polymers79,0642
Non-polymers3743
Water5,603311
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9064
Polymers39,5321
Non-polymers3743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.183, 93.957, 75.391
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 39532.004 Da / Num. of mol.: 2 / Fragment: residues 42-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-6B8 / (2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid


Mass: 259.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG5000MME, Ammonium sulfate / PH range: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56440 / % possible obs: 98.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/av σ(I): 19.95 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.037.40.429197.2
2.03-2.077.40.359198.5
2.07-2.117.40.321197.7
2.11-2.157.50.289197.6
2.15-2.27.40.266198.5
2.2-2.257.40.242198.3
2.25-2.317.50.212198.1
2.31-2.377.50.191198.3
2.37-2.447.50.175198.4
2.44-2.527.50.157198.5
2.52-2.617.50.138198.7
2.61-2.717.50.123198.8
2.71-2.847.50.11199
2.84-2.997.40.096199
2.99-3.177.40.086199
3.17-3.427.30.073199.2
3.42-3.767.30.065199.3
3.76-4.317.20.055199.5
4.31-5.437.30.053199.5
5.43-37.247.20.054198.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYN

3vyn


Resolution: 2.003→37.242 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2811 4.98 %RANDOM
Rwork0.1908 ---
obs0.1926 56414 98.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.003→37.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 24 311 5623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085443
X-RAY DIFFRACTIONf_angle_d1.187453
X-RAY DIFFRACTIONf_dihedral_angle_d12.721890
X-RAY DIFFRACTIONf_chiral_restr0.05839
X-RAY DIFFRACTIONf_plane_restr0.005976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0027-2.03720.27961310.20672582X-RAY DIFFRACTION94
2.0372-2.07420.25121310.19132633X-RAY DIFFRACTION99
2.0742-2.11410.23541190.18742698X-RAY DIFFRACTION98
2.1141-2.15730.25621270.19682628X-RAY DIFFRACTION98
2.1573-2.20420.24381330.20042685X-RAY DIFFRACTION99
2.2042-2.25540.25611530.20582643X-RAY DIFFRACTION98
2.2554-2.31180.24541280.20242665X-RAY DIFFRACTION98
2.3118-2.37430.2691410.21232701X-RAY DIFFRACTION98
2.3743-2.44420.26351240.21532691X-RAY DIFFRACTION98
2.4442-2.52310.25871470.21312619X-RAY DIFFRACTION98
2.5231-2.61320.28571670.21492697X-RAY DIFFRACTION99
2.6132-2.71780.25991460.21472655X-RAY DIFFRACTION99
2.7178-2.84150.2521170.20812713X-RAY DIFFRACTION99
2.8415-2.99120.24321590.21882660X-RAY DIFFRACTION99
2.9912-3.17850.25821290.20882738X-RAY DIFFRACTION99
3.1785-3.42380.18881400.19832729X-RAY DIFFRACTION99
3.4238-3.7680.22811380.18222696X-RAY DIFFRACTION99
3.768-4.31260.20861330.16222747X-RAY DIFFRACTION100
4.3126-5.43070.16391920.15312674X-RAY DIFFRACTION99
5.4307-37.24830.19371560.17412749X-RAY DIFFRACTION99

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