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- PDB-4z7a: Structural and biochemical characterization of a non-functionally... -

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Basic information

Entry
Database: PDB / ID: 4z7a
TitleStructural and biochemical characterization of a non-functionally redundant M. tuberculosis (3,3) L,D-Transpeptidase, LdtMt5.
ComponentsMycobacterium tuberculosis (3,3)L,D-Transpeptidase type 5
KeywordsTRANSFERASE / peptidoglycan / cell wall biosynthesis / carbapenems / nitrocefin / enzyme kinetics / enzyme structure / antibiotics / cell wall
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / acyltransferase activity / cell wall organization / regulation of cell shape / 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
ACETYL GROUP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Conserved lipoprotein LprQ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBasta, L. / Ghosh, A. / Pan, Y. / Jakoncic, J. / Lloyd, E. / Townsend, G. / Lamichhane, G. / Bianchet, M.A.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis.
Authors: Brammer Basta, L.A. / Ghosh, A. / Pan, Y. / Jakoncic, J. / Lloyd, E.P. / Townsend, C.A. / Lamichhane, G. / Bianchet, M.A.
#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
DepositionApr 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycobacterium tuberculosis (3,3)L,D-Transpeptidase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3285
Polymers47,9331
Non-polymers3954
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mycobacterium tuberculosis (3,3)L,D-Transpeptidase type 5
hetero molecules

A: Mycobacterium tuberculosis (3,3)L,D-Transpeptidase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,65610
Polymers95,8652
Non-polymers7918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area4240 Å2
ΔGint-45 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.026, 101.026, 192.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mycobacterium tuberculosis (3,3)L,D-Transpeptidase type 5


Mass: 47932.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: lprQ, MRA_0490 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5TZL1

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / Details: growth in a week

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2013
RadiationMonochromator: monocromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 41222 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 57.3
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUR

3tur


Resolution: 1.98→28.922 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 2040 4.98 %random selection
Rwork0.2198 ---
obs0.2219 40931 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→28.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 25 162 2902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062838
X-RAY DIFFRACTIONf_angle_d1.0713881
X-RAY DIFFRACTIONf_dihedral_angle_d13.1691002
X-RAY DIFFRACTIONf_chiral_restr0.038421
X-RAY DIFFRACTIONf_plane_restr0.005509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02610.38621330.30692494X-RAY DIFFRACTION98
2.0261-2.07670.3041400.31772528X-RAY DIFFRACTION99
2.0767-2.13290.31351100.27822566X-RAY DIFFRACTION99
2.1329-2.19560.31531380.2732558X-RAY DIFFRACTION99
2.1956-2.26640.3251330.29282530X-RAY DIFFRACTION99
2.2664-2.34740.32311360.27532558X-RAY DIFFRACTION99
2.3474-2.44130.32381340.27062554X-RAY DIFFRACTION100
2.4413-2.55240.28781380.26552566X-RAY DIFFRACTION100
2.5524-2.68690.30281260.25562586X-RAY DIFFRACTION99
2.6869-2.85510.2841410.26272565X-RAY DIFFRACTION99
2.8551-3.07530.31251460.2572595X-RAY DIFFRACTION99
3.0753-3.38430.29651450.22892618X-RAY DIFFRACTION100
3.3843-3.87310.26361260.20832653X-RAY DIFFRACTION99
3.8731-4.87590.18931350.16272680X-RAY DIFFRACTION100
4.8759-28.92520.2221590.18092840X-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)
10.30090.01920.10080.3313-0.6030.4838-0.0542-0.37-0.11320.3839-0.0543-0.0012-0.5091-0.29940.00040.81030.2106-0.04790.64350.08410.473-42.8519-12.9642-26.0427
21.5581-0.20050.48640.3430.21990.7671-0.3770.24080.1949-0.0519-0.0390.0197-0.58110.1387-0.37530.4267-0.0789-0.18180.4690.09430.4049-20.1203-26.14280.7938
30.30150.58690.32870.36040.08790.5327-0.21610.104-0.20030.10330.2139-0.1323-0.1650.4733-0.02980.196-0.0776-0.06840.7744-0.02190.4432-0.5379-42.179414.3852
40.07580.1053-0.09980.0732-0.15540.2525-0.438-0.10270.36110.229-0.0611-0.2398-0.95380.4313-0.03560.7241-0.1711-0.30250.5276-0.00430.5851-12.5525-22.459112.9177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 154)
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 261)
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 387 )
4X-RAY DIFFRACTION4chain 'A' and (resid 388 through 416)

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