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- PDB-5dcc: X-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDA... -

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Basic information

Entry
Database: PDB / ID: 5dcc
TitleX-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / L / D -Transpeptidase / CARBAPENEMS TEBIPENEM-ADDUCT
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / 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
(4S)-4-methyl-2,5,7-trioxoheptanoic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.451 Å
AuthorsPan, Y. / Basta, L. / Lamichhane, G. / Bianchet, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI111739 United States
Citation
Journal: BMC Biochem. / Year: 2017
Title: Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.
Authors: Bianchet, M.A. / Pan, Y.H. / Basta, L.A.B. / Saavedra, H. / Lloyd, E.P. / Kumar, P. / Mattoo, R. / Townsend, C.A. / Lamichhane, G.
#1: Journal: 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
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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
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)79,32435
Polymers75,5882
Non-polymers3,73633
Water7,368409
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,62617
Polymers37,7941
Non-polymers1,83216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,69818
Polymers37,7941
Non-polymers1,90417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.934, 94.400, 75.385
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37793.934 Da / Num. of mol.: 2 / Fragment: UNP Residues 56-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli (E. coli)
References: UniProt: O53223, UniProt: I6Y9J2*PLUS, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 7 types, 442 molecules

#2: Chemical ChemComp-58U / (4S)-4-methyl-2,5,7-trioxoheptanoic acid


Mass: 186.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG MONOMETHYLESTER 5500 18 % w/v 0.2 M AmSulphate 25 mM Tris HCl
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5146 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5146 Å / Relative weight: 1
ReflectionResolution: 2.45→43.165 Å / Num. obs: 31118 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rsym value: 0.063 / Net I/av σ(I): 43.17 / Net I/σ(I): 18.9
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.7 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5DC2

5dc2


Resolution: 2.451→43.165 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 6107 10.01 %random selectiom
Rwork0.1684 ---
obs0.173 61039 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.451→43.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 216 409 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045735
X-RAY DIFFRACTIONf_angle_d0.7257801
X-RAY DIFFRACTIONf_dihedral_angle_d13.1972021
X-RAY DIFFRACTIONf_chiral_restr0.028853
X-RAY DIFFRACTIONf_plane_restr0.0031012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4511-2.47890.27431850.20821651X-RAY DIFFRACTION89
2.4789-2.50810.33072010.21361807X-RAY DIFFRACTION97
2.5081-2.53870.26722090.20291801X-RAY DIFFRACTION98
2.5387-2.57080.28242140.20491804X-RAY DIFFRACTION99
2.5708-2.60460.25752160.19181830X-RAY DIFFRACTION99
2.6046-2.64030.26482050.20581820X-RAY DIFFRACTION99
2.6403-2.6780.27471640.20261884X-RAY DIFFRACTION99
2.678-2.7180.27122080.21041785X-RAY DIFFRACTION99
2.718-2.76050.2732100.19761834X-RAY DIFFRACTION99
2.7605-2.80570.24111810.20391880X-RAY DIFFRACTION99
2.8057-2.85410.28411910.2231853X-RAY DIFFRACTION100
2.8541-2.9060.27012140.19851832X-RAY DIFFRACTION100
2.906-2.96180.24251750.1951849X-RAY DIFFRACTION99
2.9618-3.02230.23591840.19751868X-RAY DIFFRACTION100
3.0223-3.0880.22441860.18681823X-RAY DIFFRACTION100
3.088-3.15980.25732110.18651825X-RAY DIFFRACTION99
3.1598-3.23880.20572100.17811882X-RAY DIFFRACTION100
3.2388-3.32630.21521790.17551853X-RAY DIFFRACTION100
3.3263-3.42420.22932510.17081831X-RAY DIFFRACTION100
3.4242-3.53460.18542150.16221801X-RAY DIFFRACTION100
3.5346-3.66090.18181800.16721888X-RAY DIFFRACTION100
3.6609-3.80740.21192010.15721849X-RAY DIFFRACTION100
3.8074-3.98060.21862250.15651821X-RAY DIFFRACTION100
3.9806-4.19030.19362140.14571826X-RAY DIFFRACTION100
4.1903-4.45260.16312050.12961867X-RAY DIFFRACTION100
4.4526-4.79590.18522140.11811810X-RAY DIFFRACTION100
4.7959-5.27780.16332200.13341851X-RAY DIFFRACTION100
5.2778-6.03970.16752020.13961841X-RAY DIFFRACTION100
6.0397-7.60270.18562310.15521838X-RAY DIFFRACTION100
7.6027-43.1720.17462060.15331828X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63330.10430.64452.28551.1252.2391-0.0308-0.0505-0.0480.13680.04170.06230.03460.0444-0.03440.1376-0.01850.02880.13270.02460.1916.78711.2743108.2742
20.3979-0.45310.02240.5456-0.17541.51110.0903-0.0232-0.0669-0.0355-0.05340.07250.0155-0.0207-0.03710.2129-0.063-0.01020.22150.00080.251110.9007-13.244565.7103
30.30380.0873-0.67070.5887-0.62872.55860.0136-0.08910.03450.02960.05820.03320.0459-0.0227-0.07020.149-0.0334-0.02060.1665-0.02420.1742-14.1534-22.367358.6599
42.2024-0.26990.38611.28590.27351.29910.11430.37390.0887-0.1278-0.19480.063-0.1164-0.04870.09290.19690.03390.01520.18060.02040.1868-17.3501-11.022821.0169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 407 )
3X-RAY DIFFRACTION3chain 'B' and (resid 56 through 248 )
4X-RAY DIFFRACTION4chain 'B' and (resid 249 through 408 )

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