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- PDB-7nt0: Drosophila PGRP-LB Y78F mutant in complex with tracheal cytotoxin... -

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Basic information

Entry
Database: PDB / ID: 7nt0
TitleDrosophila PGRP-LB Y78F mutant in complex with tracheal cytotoxin (TCT)
ComponentsIsoform A of Peptidoglycan-recognition protein LB
KeywordsIMMUNE SYSTEM / Peptidoglycan recognition protein / PGRP / PGRP-LB / Drosophila
Function / homology
Function and homology information


negative regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / negative regulation of peptidoglycan recognition protein signaling pathway / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / extracellular region / zinc ion binding
Similarity search - Function
Peptidoglycan recognition protein, PGRP-S / Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
Chem-MLD / Peptidoglycan-recognition protein LB
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOrlans, J. / Aller, P. / Da Silva, P.
CitationJournal: Int J Mol Sci / Year: 2021
Title: PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction.
Authors: Orlans, J. / Vincent-Monegat, C. / Rahioui, I. / Sivignon, C. / Butryn, A. / Soulere, L. / Zaidman-Remy, A. / Orville, A.M. / Heddi, A. / Aller, P. / Da Silva, P.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Isoform A of Peptidoglycan-recognition protein LB
BBB: Isoform A of Peptidoglycan-recognition protein LB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5176
Polymers47,5422
Non-polymers1,9754
Water3,405189
1
AAA: Isoform A of Peptidoglycan-recognition protein LB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7583
Polymers23,7711
Non-polymers9872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Isoform A of Peptidoglycan-recognition protein LB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7583
Polymers23,7711
Non-polymers9872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.587, 52.167, 55.579
Angle α, β, γ (deg.)92.113, 105.123, 111.513
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 176 / Label seq-ID: 5 - 178

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Isoform A of Peptidoglycan-recognition protein LB / PGRP-LB


Mass: 23771.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Please can you count the first two residue as -1 and -2 because they belong to the cleavage site of the tag. The number 1 of the sequence would be third residue.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PGRP-LB, CG14704 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8INK6, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLD / GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA / 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE


Mass: 921.899 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H59N7O20 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% v/v 2-Propanol, 100 mM Tris base HCl pH 8.5, 30% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2019
RadiationMonochromator: Double crystals monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.8→53.07 Å / Num. obs: 34852 / % possible obs: 97.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.05 / Rrim(I) all: 0.098 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-53.077.10.0452870.9970.0260.052
1.8-1.846.80.47820380.8910.2890.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimless0.7.4data reduction
DIALSdata processing
Cootmodel building
GDAdata collection
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHT

1oht


Resolution: 1.8→53.067 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.145 / SU B: 1.98 / SU ML: 0.061 / Average fsc free: 0.9498 / Average fsc work: 0.9602 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1798 1760 5.05 %
Rwork0.1447 33091 -
all0.146 --
obs-34851 97.742 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.659 Å20.031 Å2-0.431 Å2
2--0.125 Å2-0.47 Å2
3----0.223 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 72 189 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132803
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172505
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6393811
X-RAY DIFFRACTIONr_angle_other_deg1.4791.5795771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46620.872149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6861516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined0.2130.2557
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22398
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21400
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3330.24
X-RAY DIFFRACTIONr_nbd_other0.1790.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.213
X-RAY DIFFRACTIONr_mcbond_it1.9111.8471368
X-RAY DIFFRACTIONr_mcbond_other1.9111.8471368
X-RAY DIFFRACTIONr_mcangle_it2.5672.7491702
X-RAY DIFFRACTIONr_mcangle_other2.5662.7491703
X-RAY DIFFRACTIONr_scbond_it2.9072.181435
X-RAY DIFFRACTIONr_scbond_other2.9062.181436
X-RAY DIFFRACTIONr_scangle_it4.3833.1622104
X-RAY DIFFRACTIONr_scangle_other4.3823.1632105
X-RAY DIFFRACTIONr_lrange_it5.58722.5473189
X-RAY DIFFRACTIONr_lrange_other5.55522.3853166
X-RAY DIFFRACTIONr_ncsr_local_group_10.0510.055702
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.051390.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.051390.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.2161240.18724250.18926270.9160.92797.03080.177
1.847-1.8970.2291280.17123320.17425470.9230.94496.58420.16
1.897-1.9520.2211220.16122630.16424790.9280.94696.20820.148
1.952-2.0120.1951370.15522470.15724690.9440.95796.55730.143
2.012-2.0780.187980.15421950.15623520.9430.95597.49150.143
2.078-2.1510.2041170.14720980.1522720.9460.95897.49120.136
2.151-2.2320.192900.14420350.14621810.9580.96397.43240.135
2.232-2.3230.1621030.13119410.13320920.9640.97197.70550.123
2.323-2.4260.177990.12819190.1320660.9660.97597.67670.122
2.426-2.5440.1861120.14217710.14419200.9580.96398.07290.135
2.544-2.6810.181930.14617210.14818480.9570.96398.16020.141
2.681-2.8440.21840.14216170.14517280.9480.96698.43750.14
2.844-3.0390.17820.14115550.14316640.9570.96498.37740.142
3.039-3.2820.156840.13814360.13915450.9670.97198.38190.142
3.282-3.5940.169720.13713000.13813820.9640.97399.27640.143
3.594-4.0160.161650.14211880.14312670.9710.97498.8950.152
4.016-4.6330.148520.11610680.11711260.9750.98399.46710.127
4.633-5.6630.174380.1459020.1469480.9690.97999.15610.161
5.663-7.9630.254330.1976930.1997300.9450.9699.45210.213
7.963-53.0670.126270.1623850.1594130.9720.96899.75790.204

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