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- PDB-5dc2: X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDU... -

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Basic information

Entry
Database: PDB / ID: 5dc2
TitleX-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / L / D-Transpeptidase / CARBAPENEMS BIAPENEM-ADDUCT / LDTMT2 / MYCOBACTERIUM TUBERCULOSIS
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 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / 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 / Resolution: 2.182 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 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn
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)79,21135
Polymers75,5882
Non-polymers3,62433
Water10,845602
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A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,52417
Polymers37,7941
Non-polymers1,73016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,68818
Polymers37,7941
Non-polymers1,89417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.822, 93.354, 75.243
Angle α, β, γ (deg.)90.00, 92.61, 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 (strain CDC 1551 / Oshkosh) (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, 635 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.: 10 / 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.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / 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.: 602 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.46 % / Description: Thin Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % v/v PEG MME 500 0.2 M Amonium Sulfate Tris HCl 100mM NaCl
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 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5146 Å / Relative weight: 1
ReflectionResolution: 2.05→37.015 Å / Num. obs: 47794 / % possible obs: 90.9 % / Redundancy: 3.5 % / Rsym value: 0.063 / Net I/σ(I): 193.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.36 / % possible all: 50.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.182→37.015 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4162 5.01 %random selection
Rwork0.1595 ---
obs0.162 83073 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.182→37.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 201 602 6125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095729
X-RAY DIFFRACTIONf_angle_d1.0697802
X-RAY DIFFRACTIONf_dihedral_angle_d13.0472022
X-RAY DIFFRACTIONf_chiral_restr0.057853
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1821-2.20690.26321030.18092037X-RAY DIFFRACTION76
2.2069-2.23290.23221440.17772467X-RAY DIFFRACTION91
2.2329-2.26010.25091120.17552623X-RAY DIFFRACTION96
2.2601-2.28870.24061340.16922632X-RAY DIFFRACTION96
2.2887-2.31880.26711190.16882631X-RAY DIFFRACTION97
2.3188-2.35060.24841360.19242685X-RAY DIFFRACTION96
2.3506-2.38410.27481430.18972535X-RAY DIFFRACTION97
2.3841-2.41970.30061570.17862709X-RAY DIFFRACTION96
2.4197-2.45750.2541550.18882631X-RAY DIFFRACTION98
2.4575-2.49780.26691060.17662607X-RAY DIFFRACTION96
2.4978-2.54090.24561600.18292697X-RAY DIFFRACTION98
2.5409-2.58710.27511570.1932566X-RAY DIFFRACTION97
2.5871-2.63680.31441280.18312673X-RAY DIFFRACTION98
2.6368-2.69060.26321770.18962587X-RAY DIFFRACTION96
2.6906-2.74910.27021190.19782712X-RAY DIFFRACTION98
2.7491-2.8130.30721170.2042626X-RAY DIFFRACTION96
2.813-2.88330.29781370.20512642X-RAY DIFFRACTION96
2.8833-2.96130.29611220.18842642X-RAY DIFFRACTION97
2.9613-3.04840.24741380.19082647X-RAY DIFFRACTION97
3.0484-3.14670.22391240.17642684X-RAY DIFFRACTION98
3.1467-3.25910.21121440.17172699X-RAY DIFFRACTION99
3.2591-3.38950.20441360.15582702X-RAY DIFFRACTION99
3.3895-3.54370.17511570.13882643X-RAY DIFFRACTION99
3.5437-3.73030.19951410.13592703X-RAY DIFFRACTION99
3.7303-3.96380.16581300.12782719X-RAY DIFFRACTION99
3.9638-4.26940.13041320.12122714X-RAY DIFFRACTION99
4.2694-4.69830.14031700.11062680X-RAY DIFFRACTION99
4.6983-5.37640.15271480.12952644X-RAY DIFFRACTION99
5.3764-6.7670.16911660.16372691X-RAY DIFFRACTION99
6.767-37.02040.20161500.17292683X-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)
12.8102-2.19420.44786.25722.04553.3433-0.0148-0.13120.16250.1380.0755-0.1353-0.02180.1198-0.03990.1749-0.03120.02020.17610.02260.19696.0652.8458110.701
21.7279-2.2825-0.48916.9902-2.21163.7005-0.0823-0.048-0.09330.05060.05040.0540.1455-0.19270.0470.1786-0.05090.00610.2652-0.02110.2022-14.86-28.973974.4631
31.4644-0.94012.30821.3693-1.21477.7046-0.0204-0.11650.02550.00480.07420.0203-0.1033-0.1328-0.04830.1566-0.04040.05520.2249-0.00520.22727.6863-9.763180.6064
41.5720.02520.15792.2831-0.81111.98470.19920.0588-0.1857-0.1143-0.224-0.10320.11850.07140.03190.21470.0005-0.02330.2121-0.00520.211414.0442-15.775956.9871
52.1493-0.5796-2.17580.99431.08615.61350.0332-0.0656-0.12110.023-0.00070.06390.0025-0.1882-0.01870.1826-0.0251-0.02560.15290.01390.2036-12.7768-16.655144.2525
62.20240.0780.71131.62640.55481.6520.12810.27180.1029-0.1636-0.2030.1342-0.1643-0.09570.06770.24620.03990.00960.22820.00810.2119-17.3032-10.63320.5977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 56:147
2X-RAY DIFFRACTION2chain 'B' and resseq 56:147
3X-RAY DIFFRACTION3chain 'A' and resseq 148:251
4X-RAY DIFFRACTION4chain 'A' and resseq 252:407
5X-RAY DIFFRACTION5chain 'B' and resseq 148:251
6X-RAY DIFFRACTION6chain 'B' and resseq 252:407

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