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- PDB-5e1g: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 5e1g
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208
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-T8G / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 Å
AuthorsKumar, P. / Lamichhane, G. / Ginell, S.L.
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: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)79,4493
Polymers79,0642
Non-polymers3851
Water7,152397
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9172
Polymers39,5321
Non-polymers3851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
3
A: L,D-transpeptidase 2
hetero molecules

B: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)79,4493
Polymers79,0642
Non-polymers3851
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_548-x,y-1/2,-z+31
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.283, 93.872, 75.358
Angle α, β, γ (deg.)90.00, 93.08, 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-T8G / (2~{S},3~{R},4~{R})-4-(2-cyclohexyloxy-2-oxidanylidene-ethyl)sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid


Mass: 385.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27NO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 55.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG5000MME, Ammonium sulfate / PH range: 8

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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: 1.85→50 Å / Num. obs: 71306 / % possible obs: 99 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.074 / Χ2: 0.915 / Net I/av σ(I): 23.844 / Net I/σ(I): 10.1 / Num. measured all: 517286
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.887.20.45835100.9490.1810.4920.83197.8
1.88-1.927.20.38935240.9550.1540.4190.86298.2
1.92-1.957.20.34435090.9620.1360.3710.86198.3
1.95-1.997.20.28635300.9730.1130.3080.85498.1
1.99-2.047.20.23535660.9790.0930.2530.85198.5
2.04-2.087.20.2134840.9820.0830.2260.94498.5
2.08-2.147.30.17935630.9880.0710.1930.90998.7
2.14-2.197.30.16335360.9880.0640.1750.89198.8
2.19-2.267.30.14535490.9910.0570.1560.94498.7
2.26-2.337.30.12735510.9930.050.1370.92299
2.33-2.417.30.11435580.9940.0450.1220.90599.1
2.41-2.517.30.10135610.9940.040.1090.93399.1
2.51-2.637.30.09235780.9950.0360.0990.95199.2
2.63-2.767.30.08135950.9960.0320.0870.97299.4
2.76-2.947.30.07435750.9970.0290.0791.03899.6
2.94-3.167.30.06835980.9960.0270.0741.12499.6
3.16-3.487.30.0635980.9970.0240.0651.10199.7
3.48-3.997.10.04936120.9970.020.0520.95399.8
3.99-5.027.20.04136380.9980.0160.0440.76999.9
5.02-507.20.03836710.9970.0160.0410.67399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3vyn


Resolution: 1.852→37.243 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 3509 4.92 %RANDOM
Rwork0.1967 ---
obs0.1982 71275 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.852→37.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 26 397 5706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085443
X-RAY DIFFRACTIONf_angle_d1.1217454
X-RAY DIFFRACTIONf_dihedral_angle_d12.7911894
X-RAY DIFFRACTIONf_chiral_restr0.05839
X-RAY DIFFRACTIONf_plane_restr0.005978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8525-1.87780.21671030.2042408X-RAY DIFFRACTION87
1.8778-1.90470.27661200.22052674X-RAY DIFFRACTION98
1.9047-1.93310.28031460.21342715X-RAY DIFFRACTION98
1.9331-1.96330.29621480.22072648X-RAY DIFFRACTION98
1.9633-1.99550.25331400.20782688X-RAY DIFFRACTION98
1.9955-2.02990.25391430.20342695X-RAY DIFFRACTION99
2.0299-2.06680.22361270.20412692X-RAY DIFFRACTION98
2.0668-2.10660.2221520.19562735X-RAY DIFFRACTION99
2.1066-2.14960.26121450.20162692X-RAY DIFFRACTION99
2.1496-2.19630.24811550.21062690X-RAY DIFFRACTION99
2.1963-2.24740.22941220.20892717X-RAY DIFFRACTION99
2.2474-2.30360.23021370.20612721X-RAY DIFFRACTION99
2.3036-2.36580.25931530.212732X-RAY DIFFRACTION99
2.3658-2.43540.2671230.21492727X-RAY DIFFRACTION99
2.4354-2.5140.24171610.21982687X-RAY DIFFRACTION99
2.514-2.60390.26891400.22562748X-RAY DIFFRACTION99
2.6039-2.70810.25441430.21872720X-RAY DIFFRACTION99
2.7081-2.83130.26861440.21742714X-RAY DIFFRACTION99
2.8313-2.98050.23431350.21712752X-RAY DIFFRACTION100
2.9805-3.16720.22541450.21842764X-RAY DIFFRACTION100
3.1672-3.41150.22581350.19432766X-RAY DIFFRACTION100
3.4115-3.75460.23051450.18482746X-RAY DIFFRACTION100
3.7546-4.29720.1971620.17362753X-RAY DIFFRACTION100
4.2972-5.41130.17931550.16032756X-RAY DIFFRACTION100
5.4113-37.25030.19191300.17692826X-RAY DIFFRACTION99

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