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- PDB-2xz8: CRYSTAL STRUCTURE OF THE LFW ECTODOMAIN OF THE PEPTIDOGLYCAN RECO... -

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Basic information

Entry
Database: PDB / ID: 2xz8
TitleCRYSTAL STRUCTURE OF THE LFW ECTODOMAIN OF THE PEPTIDOGLYCAN RECOGNITION PROTEIN LF
ComponentsPEPTIDOGLYCAN-RECOGNITION PROTEIN LF
KeywordsIMMUNE SYSTEM / DROSOPHILA / INNATE IMMUNITY / PGRP-LF
Function / homology
Function and homology information


Antimicrobial peptides / negative regulation of peptidoglycan recognition protein signaling pathway / defense response to other organism / negative regulation of immune response / determination of adult lifespan / response to bacterium / antibacterial humoral response / innate immune response / signaling receptor binding / zinc ion binding / plasma membrane
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidoglycan-recognition protein LF
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBasbous, N. / Coste, F. / Leone, P. / Vincentelli, R. / Royet, J. / Kellenberger, C. / Roussel, A.
CitationJournal: Embo Rep. / Year: 2011
Title: The Drosophila Peptidoglycan-Recognition Protein Lf Interacts with Peptidoglycan-Recognition Protein Lc to Downregulate the Imd Pathway.
Authors: Basbous, N. / Coste, F. / Leone, P. / Vincentelli, R. / Royet, J. / Kellenberger, C. / Roussel, A.
History
DepositionNov 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
B: PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4447
Polymers33,9082
Non-polymers5365
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-5.4 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.240, 82.240, 178.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-1368-

NA

21A-2001-

HOH

31A-2070-

HOH

41A-2099-

HOH

51B-2048-

HOH

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Components

#1: Protein PEPTIDOGLYCAN-RECOGNITION PROTEIN LF / PGRP-LIKE PROTEIN / PGRP-LF


Mass: 16954.184 Da / Num. of mol.: 2 / Fragment: LFW ECTODOMAIN, RESIDUES 230-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI / References: UniProt: Q8SXQ7
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 3.8 / Details: 45% PEG 300, 0.1M PHOSPHATE CITRATE PH 3.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 24, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.94→37.82 Å / Num. obs: 27070 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F2L (CHAIN A)

2f2l


Resolution: 1.94→35.611 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 1356 5 %
Rwork0.1735 --
obs0.1752 27026 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.747 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.9046 Å20 Å20 Å2
2--1.9046 Å20 Å2
3----8.6469 Å2
Refinement stepCycle: LAST / Resolution: 1.94→35.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 35 180 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072162
X-RAY DIFFRACTIONf_angle_d1.0152944
X-RAY DIFFRACTIONf_dihedral_angle_d16.086766
X-RAY DIFFRACTIONf_chiral_restr0.072335
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.00930.22141350.19942490X-RAY DIFFRACTION98
2.0093-2.08980.19841240.17732493X-RAY DIFFRACTION99
2.0898-2.18490.18561360.16812508X-RAY DIFFRACTION99
2.1849-2.30.2081290.16362507X-RAY DIFFRACTION99
2.3-2.44410.19831550.16052505X-RAY DIFFRACTION99
2.4441-2.63280.20791400.1642543X-RAY DIFFRACTION99
2.6328-2.89760.21541370.16582568X-RAY DIFFRACTION99
2.8976-3.31660.231350.172592X-RAY DIFFRACTION100
3.3166-4.17760.17661420.14722649X-RAY DIFFRACTION100
4.1776-35.61690.23521230.19532815X-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)
11.9195-0.55592.15380.7197-0.90281.6130.02120.38270.0328-0.0107-0.116-0.17670.10980.1130.0810.10610.03740.01890.1881-0.00920.091416.523739.285594.6827
20.4446-1.125-0.9482.6681.39790.8829-0.05690.1073-0.09090.3821-0.04150.25880.28180.10510.05350.27540.1-0.01870.1838-0.00550.149212.865943.878178.0846
34.5609-5.60732.4254-1.3518-3.36855.0262-0.9909-0.61481.73740.0628-0.1637-0.2533-1.4941-0.60040.88840.44480.0959-0.15890.2642-0.14680.380415.738258.004695.6454
40.7274-0.8063-0.2259-0.5128-0.28542.1049-0.0217-0.04090.13410.0698-0.023-0.0259-0.2321-0.18180.05590.13750.0354-0.03850.1223-0.01150.132310.924847.845399.3777
5-0.3518-0.12660.51841.3076-0.3281.5018-0.02430.0177-0.00150.0334-0.1137-0.1293-0.0170.28020.12420.10430.0063-0.00180.13550.01910.110616.852646.908991.1233
61.98331.87271.55122.5702-3.08337.2898-0.2306-0.1352-0.1056-0.3590.42310.08420.5776-0.68430.03840.15350.0034-0.0070.1911-0.03230.13948.74940.520884.5017
71.2929-0.0416-0.9510.6338-1.48073.58430.20380.04750.20810.0276-0.2962-0.178-0.62390.14470.0340.22790.00950.01340.15370.05940.186518.338453.130584.5488
80.8996-0.71061.37431.6661.27422.6504-0.09990.09140.00790.47180.101-0.19010.63780.7584-0.03150.2740.15940.01650.26380.0550.171123.752342.195377.4005
92.59141.4663-0.36696.8036-3.65115.44180.42581.29580.3095-1.5258-0.9328-0.34250.7515-0.62020.36450.4380.25290.00210.45180.08020.152417.711643.726171.356
103.5254-0.37491.1456-0.0968-1.04653.0689-0.37410.27760.34870.06040.244-0.0794-0.34810.09230.09330.26290.1089-0.05750.16370.01590.156310.147855.407679.1344
111.2135-0.3968-0.93870.39410.69231.2796-0.04040.14640.009-0.0771-0.03410.1019-0.1917-0.0590.06060.15060.0135-0.00580.1459-0.01080.136823.727531.339893.9112
120.9198-0.70190.14490.9080.42970.17980.18880.1852-0.0512-0.297-0.2765-0.04440.14150.20130.05930.27260.1184-0.00050.2025-0.01590.176627.73221.734181.989
132.0598-3.9488-2.15122.11114.43186.0286-0.1819-0.3415-0.75360.8826-0.47370.41251.73380.26440.4930.70520.04850.13910.27210.10460.342621.668213.1791100.0202
140.8793-1.07780.06220.81321.12213.8757-0.0511-0.3526-0.20380.27220.013-0.0930.5190.67360.03970.18440.09310.03780.17990.02130.111830.519323.5852100.0428
151.24010.0274-0.21391.74981.27681.3577-0.0290.0715-0.00370.2077-0.11360.20390.2167-0.05180.11640.12040.00740.01690.0984-0.01970.109723.425423.130892.2363
161.68650.3306-2.80293.08492.47254.83540.2396-0.18280.1383-0.46140.0416-0.1381-0.26880.5804-0.12360.06340.01940.00570.10740.01440.121130.403929.582986.0108
170.8487-0.11551.49012.812-0.60761.9566-0.07050.3281-0.04070.1462-0.1599-0.27220.03370.44970.11540.21130.03440.01370.2082-0.02240.155528.600622.522184.5834
183.9181-1.25950.4903-2.51242.35315.3370.1492-0.0163-0.95071.07770.17040.51532.1379-0.1828-0.19480.7506-0.0097-0.06440.1774-0.05710.432319.425712.692986.9363
190.593-0.158-0.06572.40931.42522.37150.15670.1883-0.28-0.4101-0.51760.1592-0.1453-0.49770.27650.26360.0996-0.05650.2473-0.11520.224216.804825.310178.1909
202.0672-1.9922-1.01384.85450.06511.5015-0.19490.39350.01420.1515-0.2712-0.2668-0.26230.07310.26170.40750.15840.03010.194-0.04850.197328.0616.61278.0797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 234:254)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 255:26)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 265:273)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 274:295)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 296:314)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 315:326)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 327:346)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 347:355)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 356:360)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 361:368)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 231:252)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 253:264)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 265:271)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 272:292)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 293:311)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 312:320)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 321:330)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 331:342)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 343:355)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 356:364)

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