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- PDB-5e5l: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 5e5l
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 Angstrom
ComponentsL,D-transpeptidase 1
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 / periplasmic space / extracellular region
Similarity search - Function
Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain ...Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
L,D-transpeptidase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 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 1.5Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L,D-transpeptidase 1
B: L,D-transpeptidase 1
C: L,D-transpeptidase 1
D: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)95,8684
Polymers95,8684
Non-polymers00
Water6,449358
1
A: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: L,D-transpeptidase 1


Theoretical massNumber of molelcules
Total (without water)23,9671
Polymers23,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.731, 57.731, 256.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
L,D-transpeptidase 1 / LDT 1 / Ldt(Mt1)


Mass: 23966.965 Da / Num. of mol.: 4 / Fragment: Residues 32-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ldtA, Rv0116c, RVBD_0116c, P425_00122 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53638, Transferases; Acyltransferases; Aminoacyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG6000, Bicine / PH range: pH 9.0

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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: Apr 17, 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
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.89→24.54 Å / Num. obs: 72790 / % possible obs: 98.6 % / Redundancy: 13 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Rrim(I) all: 0.125 / Χ2: 0.984 / Net I/av σ(I): 18.615 / Net I/σ(I): 8.8 / Num. measured all: 317362
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.89-1.9312.511770.7680.4080.792100
1.82-1.8510.111950.8080.3920.794100
1.85-1.8911.511960.8460.4040.881100
1.89-1.9312.511970.8620.1571.0611000.5370.56
1.93-1.971412070.9120.2040.8641000.7430.771
1.97-2.0214.311900.9350.1330.8771000.4890.507
2.02-2.0714.212210.9520.1070.8911000.3940.409
2.07-2.1214.511910.9610.0980.90699.80.3640.377
2.12-2.1814.212010.9680.0920.9391000.3360.348
2.18-2.2614.212090.9780.0771.3961000.2810.292
2.26-2.3414.412160.9890.0671.0281000.2430.252
2.34-2.4314.212190.990.0510.91000.1860.193
2.43-2.5414.312220.9920.0430.9171000.1540.16
2.54-2.6714.112290.9930.0380.9721000.1350.14
2.67-2.8414.112470.9940.0331.0171000.1170.122
2.84-3.061412300.9910.031.0599.50.1050.109
3.06-3.3713.412730.9920.0271.00499.50.0940.098
3.37-3.861212270.9830.031.08996.30.0960.1
3.86-4.8610.912080.9830.0311.15792.10.0970.103
4.86-501112850.9870.0311.05587.20.0970.103

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIX(phenix.refine: 1.9_1692)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JMN

3jmn


Resolution: 1.89→24.537 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.83 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2569 3880 2.72 %
Rwork0.2085 --
obs0.2139 142624 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→24.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5866 0 0 358 6224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016026
X-RAY DIFFRACTIONf_angle_d1.4168253
X-RAY DIFFRACTIONf_dihedral_angle_d12.4442062
X-RAY DIFFRACTIONf_chiral_restr0.059954
X-RAY DIFFRACTIONf_plane_restr0.0091049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8908-1.92340.27471120.29013976X-RAY DIFFRACTION51
1.9234-1.95840.27251280.2724642X-RAY DIFFRACTION63
1.9584-1.9960.37751840.26716164X-RAY DIFFRACTION79
1.996-2.03670.25371920.266792X-RAY DIFFRACTION90
2.0367-2.08090.26662160.25597338X-RAY DIFFRACTION96
2.0809-2.12930.30272200.25337430X-RAY DIFFRACTION97
2.1293-2.18250.29041960.25187336X-RAY DIFFRACTION97
2.1825-2.24140.32282120.25137490X-RAY DIFFRACTION97
2.2414-2.30730.33172080.26267540X-RAY DIFFRACTION97
2.3073-2.38170.28852080.24017360X-RAY DIFFRACTION97
2.3817-2.46660.29712000.24097374X-RAY DIFFRACTION97
2.4666-2.56520.25651960.22787384X-RAY DIFFRACTION97
2.5652-2.68170.27752080.23997478X-RAY DIFFRACTION97
2.6817-2.82280.24852240.22977402X-RAY DIFFRACTION97
2.8228-2.99910.24782080.21597418X-RAY DIFFRACTION97
2.9991-3.22980.23942140.20087484X-RAY DIFFRACTION97
3.2298-3.55330.23781960.1867328X-RAY DIFFRACTION96
3.5533-4.06380.23631720.16697006X-RAY DIFFRACTION92
4.0638-5.10650.22381920.13926872X-RAY DIFFRACTION90
5.1065-20.28570.2151940.18356802X-RAY DIFFRACTION89

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