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- PDB-7nsy: Drosophila PGRP-LB C160S mutant -

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Basic information

Entry
Database: PDB / ID: 7nsy
TitleDrosophila PGRP-LB C160S mutant
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
Peptidoglycan-recognition protein LB
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)47,5422
Polymers47,5422
Non-polymers00
Water4,738263
1
AAA: Isoform A of Peptidoglycan-recognition protein LB


Theoretical massNumber of molelcules
Total (without water)23,7711
Polymers23,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Isoform A of Peptidoglycan-recognition protein LB


Theoretical massNumber of molelcules
Total (without water)23,7711
Polymers23,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.020, 49.187, 52.143
Angle α, β, γ (deg.)71.822, 79.001, 66.840
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: ARG / Beg label comp-ID: ARG / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 14 - 177 / Label seq-ID: 16 - 179

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: 23770.965 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium thiocyanate, 20%c w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→49.39 Å / Num. obs: 67209 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-49.393.40.0194210.9990.0190.027
1.4-1.422.60.2632180.8750.260.368

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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: 1.4→49.39 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.887 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.058
RfactorNum. reflection% reflection
Rfree0.1879 3360 5 %
Rwork0.1666 63841 -
all0.168 --
obs-67201 96.044 %
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: 17.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.225 Å20.172 Å20.476 Å2
2--0.718 Å2-0.003 Å2
3----0.437 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 0 263 2846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132700
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172418
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.6383678
X-RAY DIFFRACTIONr_angle_other_deg1.5651.585570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15220.791139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48815400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6271518
X-RAY DIFFRACTIONr_chiral_restr0.110.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined0.2170.2534
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22278
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21325
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2147
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.23
X-RAY DIFFRACTIONr_nbd_other0.1550.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.216
X-RAY DIFFRACTIONr_mcbond_it1.581.6191342
X-RAY DIFFRACTIONr_mcbond_other1.5811.6171341
X-RAY DIFFRACTIONr_mcangle_it2.1942.4261677
X-RAY DIFFRACTIONr_mcangle_other2.1932.4281678
X-RAY DIFFRACTIONr_scbond_it2.6681.9081358
X-RAY DIFFRACTIONr_scbond_other2.6671.9091358
X-RAY DIFFRACTIONr_scangle_it3.8842.771995
X-RAY DIFFRACTIONr_scangle_other3.8842.771995
X-RAY DIFFRACTIONr_lrange_it4.90519.9993098
X-RAY DIFFRACTIONr_lrange_other4.81819.6313056
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.055461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.071970.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.071970.05009
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
1.4-1.4360.3132320.24345850.24651950.8390.87792.72380.233
1.436-1.4760.2292240.21445260.21550560.9110.91393.94780.201
1.476-1.5180.2182090.18744240.18849030.9270.93794.49320.175
1.518-1.5650.2051960.18443150.18547600.9360.9494.76890.171
1.565-1.6160.1992220.1841630.18146240.9350.94394.83130.169
1.616-1.6730.2152220.17440200.17644420.9370.94895.49750.165
1.673-1.7360.1822190.16238780.16342880.9540.95795.54570.154
1.736-1.8070.1862190.16138100.16341980.9520.95895.97430.156
1.807-1.8870.1881890.15936160.1639470.9540.9696.40230.154
1.887-1.9790.1631860.15234690.15237890.9640.96696.46340.15
1.979-2.0860.1681930.15133360.15236370.9630.96797.03050.153
2.086-2.2120.1611760.14631430.14734120.9680.97197.27430.151
2.212-2.3650.161440.15229820.15232030.9660.96697.5960.16
2.365-2.5540.1691560.15527620.15629810.9620.96597.88660.166
2.554-2.7970.1911310.15325720.15527560.9530.96298.07690.169
2.797-3.1250.1981120.1623510.16124990.950.96398.55940.179
3.125-3.6070.1811070.16220440.16321800.9590.96298.66970.185
3.607-4.4110.179970.16317500.16418640.9630.9699.0880.195
4.411-6.2140.195820.18713470.18814360.9520.95999.51250.226
6.214-49.390.283440.2327480.2357990.8880.93299.12390.368

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