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- PDB-2xz4: Crystal structure of the LFZ ectodomain of the peptidoglycan reco... -

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Basic information

Entry
Database: PDB / ID: 2xz4
TitleCrystal structure of the LFZ ectodomain of the peptidoglycan recognition protein LF
ComponentsPEPTIDOGLYCAN-RECOGNITION PROTEIN LF
KeywordsIMMUNE SYSTEM / INNATE IMMUNITY
Function / homology
Function and homology information


Antimicrobial peptides / negative regulation of peptidoglycan recognition protein signaling pathway / defense response to other organism / peptidoglycan immune receptor activity / negative regulation of immune response / detection of bacterium / determination of adult lifespan / response to bacterium / antibacterial humoral response / defense response to Gram-positive bacterium ...Antimicrobial peptides / negative regulation of peptidoglycan recognition protein signaling pathway / defense response to other organism / peptidoglycan immune receptor activity / negative regulation of immune response / detection of bacterium / determination of adult lifespan / response to bacterium / antibacterial humoral response / defense response to Gram-positive bacterium / 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
Chem-1PG / COPPER (II) ION / Peptidoglycan-recognition protein LF
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 23, 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)41,6999
Polymers41,0732
Non-polymers6267
Water4,107228
1
A: PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9765
Polymers20,5361
Non-polymers4404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7234
Polymers20,5361
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.802, 113.443, 37.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-500-

CU

21A-2004-

HOH

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Components

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


Mass: 20536.312 Da / Num. of mol.: 2 / Fragment: LFZ ECTODOMAIN, RESIDUES 52-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PMT/BIP/V5-HISA / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q8SXQ7
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLFZ IS THE FIRST PGRP ECTODOMAIN OF PGRP-LF

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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: 1.94 Å3/Da / Density % sol: 36.55 % / Description: NONE
Crystal growpH: 6 / Details: 30% PEG300, 0.1M SODIUM CACODYLATE PH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2011 / 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: 1.72→45.17 Å / Num. obs: 34205 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.97 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 96.5

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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 X

2f2l


Resolution: 1.72→33.747 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1718 5 %
Rwork0.1636 --
obs0.1655 34162 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.451 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.7313 Å2-0 Å20 Å2
2---3.1114 Å20 Å2
3---2.3802 Å2
Refinement stepCycle: LAST / Resolution: 1.72→33.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 35 228 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072726
X-RAY DIFFRACTIONf_angle_d1.0843682
X-RAY DIFFRACTIONf_dihedral_angle_d13.708990
X-RAY DIFFRACTIONf_chiral_restr0.077375
X-RAY DIFFRACTIONf_plane_restr0.005477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.78150.23711470.21533114X-RAY DIFFRACTION95
1.7815-1.85280.26061560.18183231X-RAY DIFFRACTION100
1.8528-1.93710.22041910.16723221X-RAY DIFFRACTION100
1.9371-2.03930.20311810.16063250X-RAY DIFFRACTION100
2.0393-2.1670.19911810.14793243X-RAY DIFFRACTION100
2.167-2.33430.18341710.14343277X-RAY DIFFRACTION99
2.3343-2.56910.19851760.15133245X-RAY DIFFRACTION99
2.5691-2.94070.20361810.16143262X-RAY DIFFRACTION98
2.9407-3.70420.16371770.15023287X-RAY DIFFRACTION98
3.7042-33.75370.20151570.16463314X-RAY DIFFRACTION94
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)
10.6359-0.30240.73981.2636-0.1970.87080.17110.267-0.3652-0.04010.0437-0.4848-0.0710.2281-0.13750.0428-0.0024-0.00970.1167-0.02680.28133.85973.63016.3186
20.5627-0.79280.20841.89880.27950.5144-0.0105-0.18610.1470.38350.1418-0.7059-0.02150.2209-0.05130.2073-0.0099-0.11360.1056-0.03630.141529.57878.361719.4018
31.0735-1.21360.13893.25560.05120.3084-0.00720.0915-0.05640.24450.06650.1835-0.0212-0.0251-0.08560.0695-0.00730.00190.09040.02020.08320.4827-3.410912.0748
45.5129-1.7579-1.31185.9176-0.13060.36920.1720.75990.089-0.8336-0.2464-0.2735-0.1153-0.31310.05610.12390.01950.01660.1760.03590.127926.61537.211-2.5889
50.56130.00620.37351.01150.21720.649-0.05630.01050.16830.08610.1009-0.2069-0.0925-0.0008-0.02480.09970.0254-0.02230.12560.00790.147421.757611.998610.6234
60.52460.2396-0.44170.9044-0.10590.75540.07530.08480.05590.0916-0.0423-0.133-0.0683-0.08210.00170.09030.0148-0.03070.10450.00790.122125.15131.676212.8272
72.5183-0.8847-1.13052.0743-0.12390.8584-0.1096-0.3123-0.21910.29810.07740.39580.0212-0.14510.01740.09130.00360.02770.11150.00570.138717.0655-2.386411.3941
81.1640.05821.66324.15221.60894.3484-0.09630.0463-0.1034-0.6573-0.13810.6581-0.102-0.29960.16810.20930.0339-0.09060.2307-0.08810.215614.4981-4.4337-3.6106
90.9137-0.01011.35670.12620.25162.48170.14680.0194-0.0271-0.0455-0.1621-0.10110.2656-0.0220.00310.1210.0060.00420.1130.00420.158927.1139-9.84734.3879
102.6716-1.9356-0.07292.37420.12031.1974-0.3476-0.28380.04280.40560.3054-0.37210.22450.17490.01590.15030.0092-0.04650.1252-0.00340.146230.1996-14.706916.0462
110.10150.0072-0.23122.19510.05650.8144-0.0454-0.21-0.34730.1369-0.02220.51290.023-0.09910.09940.10010.00690.04080.136-0.00550.220411.1525-6.521413.4218
120.5446-0.50680.37620.9763-0.38550.46190.20640.1147-0.3252-0.1791-0.11820.39280.20180.0169-0.08060.1185-0.0124-0.02090.1435-0.04310.272212.774-12.31156.2937
130.63470.2781-0.00031.1486-0.04740.3154-0.0699-0.01210.0594-0.01290.1172-0.20640.0003-0.0069-0.0060.07930.0068-0.0040.14050.01630.178315.218916.87370.7579
140.8102-0.7831-0.00495.501-1.46861.62120.027-0.1138-0.1639-0.64440.17250.01760.2489-0.0723-0.12210.1894-0.0111-0.03330.1497-0.02220.13684.005711.1975-9.4669
151.7231-0.6923-0.64982.597-0.04420.251-0.1202-0.021-0.02520.08480.1010.1195-0.218-0.2343-0.05340.13460.04510.01740.13040.03010.10131.190825.276-1.4544
160.759-0.38040.40471.6005-0.22611.7395-0.2364-0.1905-0.02060.12760.03680.219-0.2104-0.05050.12110.15310.05180.02710.15770.0260.1248.822516.64358.6122
170.5343-0.3710.42930.4384-0.20931.0012-0.0221-0.0384-0.04180.07810.0111-0.0575-0.1474-0.08020.0160.117-0.0044-0.00140.10760.01150.11546.020618.6019-0.9663
180.18951.1912-0.90989.3389-4.96986.76550.1195-0.1586-0.16490.15090.26971.3132-0.162-0.4542-0.28230.1590.0345-0.02990.23830.05060.2807-3.009220.5337-8.1105
190.6469-0.2678-0.98120.31590.3321.71-0.073-0.22210.14130.41050.05280.2395-0.4766-0.2681-0.01990.37490.08590.03140.1702-0.01260.13623.801530.37628.4289
200.9290.754-0.71170.843-1.57018.78170.1087-0.27720.16410.431-0.1712-0.0886-0.89960.39920.08330.2291-0.0185-0.01340.13290.01390.190110.380833.2184-4.7539
216.28520.9123-1.82815.1878-0.59150.8768-0.05180.6583-0.163-0.6857-0.0488-0.4845-0.0429-0.04360.11920.21950.02170.02440.1443-0.00730.16669.337730.5158-14.7517
222.43352.1393-3.96634.201-4.40377.3494-0.21430.3704-0.40510.06890.33180.77860.0677-1.0245-0.0310.26070.1190.09290.20060.10180.3549-3.245332.4528-6.0597
238.2073-7.0487-2.82616.09751.94066.5075-0.6439-0.7833-1.26350.38530.26451.2928-0.4079-1.56670.37380.29910.21990.11450.50790.0080.4568-7.336430.0535.1229
240.6064-1.9649-0.69736.2492.18320.8163-0.25-0.3337-0.04330.77460.46850.00290.5162-0.031-0.18690.4030.17760.03330.29410.0210.2667-2.886338.4223-1.2427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:16)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 17:27)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 28:45)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 46:53)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 54:66)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 67:96)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 97:113)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 114:119)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 120:132)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 133:142)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 143:155)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 156:173)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 8:19)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 20:28)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 29:45)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 46:63)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 64:91)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 92:104)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 105:122)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 123:133)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 134:139)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 140:148)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 149:162)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 163:172)

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