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- PDB-8j65: the structure of L,D-transpeptidase LdtMt2 complex with citrate -

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Basic information

Entry
Database: PDB / ID: 8j65
Titlethe structure of L,D-transpeptidase LdtMt2 complex with citrate
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / L / D-transpeptidase / YkuD / citrate
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
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-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CITRIC ACID / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, D.F. / Qin, Y.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92051101 China
National Natural Science Foundation of China (NSFC)31870037 China
CitationJournal: To Be Published
Title: Citrate interacts with L,D-transpeptidase and hinders the growth of Mycobacterium
Authors: Li, D.F. / Qin, Y.L.
History
DepositionApr 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)64,4334
Polymers64,0492
Non-polymers3842
Water5,891327
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2162
Polymers32,0241
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2162
Polymers32,0241
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.184, 75.885, 67.068
Angle α, β, γ (deg.)90.00, 111.92, 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: 32024.344 Da / Num. of mol.: 2 / Mutation: a truncated mutant with residues 140-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% PEG3350, 10 mM citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→48.12 Å / Num. obs: 42144 / % possible obs: 95.6 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.038 / Rrim(I) all: 0.073 / Net I/σ(I): 18.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.784 / Num. unique obs: 2497 / CC1/2: 0.827 / Rpim(I) all: 0.314 / Rrim(I) all: 0.846 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYP

3vyp


Resolution: 1.8→48.115 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 2008 4.77 %
Rwork0.2123 --
obs0.2134 42089 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 26 327 4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044118
X-RAY DIFFRACTIONf_angle_d0.675636
X-RAY DIFFRACTIONf_dihedral_angle_d6.5572356
X-RAY DIFFRACTIONf_chiral_restr0.05604
X-RAY DIFFRACTIONf_plane_restr0.004744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.32851430.28372875X-RAY DIFFRACTION96
1.845-1.89490.31751400.26942858X-RAY DIFFRACTION96
1.8949-1.95070.29221460.25472873X-RAY DIFFRACTION96
1.9507-2.01370.28571440.24792819X-RAY DIFFRACTION96
2.0137-2.08560.29851400.23662856X-RAY DIFFRACTION95
2.0856-2.16910.25221470.22872870X-RAY DIFFRACTION96
2.1691-2.26790.26251410.22572895X-RAY DIFFRACTION97
2.2679-2.38740.28241400.22832878X-RAY DIFFRACTION96
2.3874-2.5370.2561440.21952832X-RAY DIFFRACTION94
2.537-2.73290.26711470.22582879X-RAY DIFFRACTION96
2.7329-3.00780.24221470.21472871X-RAY DIFFRACTION96
3.0078-3.4430.20741340.19442843X-RAY DIFFRACTION94
3.443-4.33730.18251460.17352885X-RAY DIFFRACTION96
4.3373-48.1150.20581490.20572847X-RAY DIFFRACTION93

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