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- PDB-5xz3: The X-ray structure of Apis mellifera PGRP-SA -

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Basic information

Entry
Database: PDB / ID: 5xz3
TitleThe X-ray structure of Apis mellifera PGRP-SA
ComponentsPeptidoglycan-recognition protein
KeywordsIMMUNE SYSTEM / Apis mellifera / PGRP-SA
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / peptidoglycan catabolic process / innate immune response / 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. / 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 ...Peptidoglycan recognition protein, PGRP-S / 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
Peptidoglycan-recognition protein
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLiu, Y.J. / Huang, J.X. / Zhao, X.M. / An, J.D.
Funding support China, 2items
OrganizationGrant numberCountry
Natural Science Foundation of ChinaNO.31672500 China
Agricultural Science and Technology Innovation ProgramCAAS-ASTIP-2015-IAR China
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structure of peptidoglycan recognition protein SA in Apis mellifera (Hymenoptera: Apidae).
Authors: Liu, Y. / Zhao, X. / Naeem, M. / An, J.
History
DepositionJul 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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
A: Peptidoglycan-recognition protein
B: Peptidoglycan-recognition protein
C: Peptidoglycan-recognition protein
D: Peptidoglycan-recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0788
Polymers78,6934
Non-polymers3844
Water4,396244
1
A: Peptidoglycan-recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7692
Polymers19,6731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area8400 Å2
MethodPISA
2
B: Peptidoglycan-recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7692
Polymers19,6731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area8190 Å2
MethodPISA
3
C: Peptidoglycan-recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7692
Polymers19,6731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area8020 Å2
MethodPISA
4
D: Peptidoglycan-recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7692
Polymers19,6731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.898, 68.607, 71.699
Angle α, β, γ (deg.)90.00, 94.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidoglycan-recognition protein


Mass: 19673.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: PGRP-S3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A088AJM6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride; 2.0 M Ammonium sulfate; PH 8.5
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50.01 Å / Num. obs: 50577 / % possible obs: 91.3 % / Redundancy: 7.4 % / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S2J

1s2j


Resolution: 1.86→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.516 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.21655 2476 4.9 %RANDOM
Rwork0.18993 ---
obs0.19138 48086 90.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.016 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å2-0 Å20.31 Å2
2--0.08 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.86→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 20 244 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9257477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.92125258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65615947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0411516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9312.7132680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4734.063343
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3332.8952833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.80337.348458
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.856→1.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 117 -
Rwork0.212 2067 -
obs--53.33 %
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)
11.0486-0.3549-0.3090.55450.42661.362-0.01360.10590.088-0.00520.0291-0.0847-0.0691-0.0758-0.01550.016-0.003-0.0160.037-0.00670.049425.6581.04424.2128
20.1939-0.149-0.10130.629-0.00181.17650.0659-0.0171-0.03810.0054-0.00150.0392-0.0072-0.0153-0.06440.0313-0.0111-0.01630.0123-0.00720.053635.240115.526930.7114
31.5744-1.18930.1551.6184-0.79861.2939-0.2534-0.1043-0.09040.20490.33010.1197-0.1254-0.1561-0.07670.07920.03110.02790.12660.0290.03172.7108-2.418839.956
40.56670.47690.28670.51140.19811.7454-0.03440.0166-0.004-0.00510.0215-0.06510.1454-0.2710.0130.0307-0.0488-0.01120.1134-0.00920.0359.1302-23.41895.8434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION2B6 - 173
3X-RAY DIFFRACTION3C9 - 173
4X-RAY DIFFRACTION4D9 - 173

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