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- PDB-7nsx: Drosophila PGRP-LB wild-type -

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Basic information

Entry
Database: PDB / ID: 7nsx
TitleDrosophila PGRP-LB wild-type
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 / zinc ion binding / extracellular region
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
Peptidoglycan-recognition protein LB
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,8522
Polymers23,7871
Non-polymers651
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.869, 70.546, 112.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23787.029 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.67 Å3/Da / Density % sol: 26.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH7.0, 30% v/v Jeffamine ED-2003

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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: Sep 27, 2018
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: 1.9→112.83 Å / Num. obs: 12942 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.073 / Rrim(I) all: 0.153 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.11-112.8360.0431500.9980.0240.049
1.9-1.947.21.1978080.5620.6991.394

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Processing

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

1oht


Resolution: 1.9→56.478 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.89 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / ESU R Free: 0.139
RfactorNum. reflection% reflection
Rfree0.2128 680 5.278 %
Rwork0.1799 12203 -
all0.182 --
obs-12883 99.667 %
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: 27.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.309 Å20 Å2-0 Å2
2--0.223 Å20 Å2
3---0.086 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 1 51 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131376
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171241
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6441869
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5812856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9125169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27420.94674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19915210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6531510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2030.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21190
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2669
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.247
X-RAY DIFFRACTIONr_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.213
X-RAY DIFFRACTIONr_nbd_other0.2030.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.26
X-RAY DIFFRACTIONr_mcbond_it2.2242.683679
X-RAY DIFFRACTIONr_mcbond_other2.2072.677678
X-RAY DIFFRACTIONr_mcangle_it3.1164.009847
X-RAY DIFFRACTIONr_mcangle_other3.1254.014848
X-RAY DIFFRACTIONr_scbond_it2.9493.061697
X-RAY DIFFRACTIONr_scbond_other2.9143.059697
X-RAY DIFFRACTIONr_scangle_it4.4314.4741022
X-RAY DIFFRACTIONr_scangle_other4.4034.4731022
X-RAY DIFFRACTIONr_lrange_it5.56631.4241531
X-RAY DIFFRACTIONr_lrange_other5.56231.3471526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.333360.279881X-RAY DIFFRACTION99.1351
1.949-2.0030.307670.248853X-RAY DIFFRACTION99.5671
2.003-2.0610.305410.218833X-RAY DIFFRACTION99.4312
2.061-2.1240.247330.217843X-RAY DIFFRACTION99.6587
2.124-2.1940.259520.209763X-RAY DIFFRACTION99.2692
2.194-2.2710.227600.199761X-RAY DIFFRACTION99.2745
2.271-2.3570.193390.19752X-RAY DIFFRACTION99.6222
2.357-2.4530.337330.188711X-RAY DIFFRACTION99.8658
2.453-2.5620.243300.189710X-RAY DIFFRACTION99.8651
2.562-2.6870.226390.187657X-RAY DIFFRACTION99.5708
2.687-2.8320.244440.173621X-RAY DIFFRACTION100
2.832-3.0040.223370.18597X-RAY DIFFRACTION100
3.004-3.2110.17280.17561X-RAY DIFFRACTION100
3.211-3.4680.14250.16536X-RAY DIFFRACTION100
3.468-3.7990.187330.161481X-RAY DIFFRACTION100
3.799-4.2460.207240.151448X-RAY DIFFRACTION100
4.246-4.9020.171230.143404X-RAY DIFFRACTION100
4.902-6.0010.1990.173357X-RAY DIFFRACTION100
6.001-8.4750.199130.198271X-RAY DIFFRACTION99.6491
8.475-56.4780.143140.15163X-RAY DIFFRACTION98.8827

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