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- PDB-5xz4: The X-tay structure of Bumblebee PGRP-SA -

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Basic information

Entry
Database: PDB / ID: 5xz4
TitleThe X-tay structure of Bumblebee PGRP-SA
ComponentsBumblebee peptidoglycan recognition protein SA
KeywordsIMMUNE SYSTEM / Bumblebee / PGRP-SA
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / 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
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesBombus (bumble bees)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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: J Immunol. / Year: 2019
Title: Structural Insights into the Preferential Binding of PGRP-SAs from Bumblebees and Honeybees to Dap-Type Peptidoglycans Rather than Lys-Type Peptidoglycans.
Authors: Liu, Y.J. / Zhao, X.M. / Huang, J.X. / Chen, M.M. / An, J.D.
History
DepositionJul 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bumblebee peptidoglycan recognition protein SA
B: Bumblebee peptidoglycan recognition protein SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9646
Polymers38,5542
Non-polymers4104
Water6,089338
1
A: Bumblebee peptidoglycan recognition protein SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5914
Polymers19,2771
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area8070 Å2
MethodPISA
2
B: Bumblebee peptidoglycan recognition protein SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3732
Polymers19,2771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.950, 49.940, 78.770
Angle α, β, γ (deg.)90.00, 120.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

#1: Protein Bumblebee peptidoglycan recognition protein SA


Mass: 19276.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombus (bumble bees) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSL6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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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: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 72461 / % possible obs: 96.6 % / Redundancy: 7.5 % / Net I/σ(I): 11.3
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.619 / % possible all: 94.6

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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: 1.41→38.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.458 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.013
RfactorNum. reflection% reflectionSelection details
Rfree0.20903 3635 5 %RANDOM
Rwork0.18501 ---
obs0.18622 68420 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.276 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å20 Å22.37 Å2
2---7.13 Å2-0 Å2
3---3.12 Å2
Refinement stepCycle: 1 / Resolution: 1.41→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 23 338 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9283641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14724.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89915454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8671514
X-RAY DIFFRACTIONr_chiral_restr0.10.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022012
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_it1.0091.1831334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.321.7731664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5881.471354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.33417.6924075
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.41532688
X-RAY DIFFRACTIONr_sphericity_free19.7815242
X-RAY DIFFRACTIONr_sphericity_bonded10.44752725
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 262 -
Rwork0.379 4917 -
obs--94.13 %
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)
10.0884-0.03840.05470.2171-0.02570.1085-0.0131-0.02460.00020.0083-0.0014-0.0111-0.0092-0.0070.01450.0025-0.0009-0.00050.0434-0.00110.0149-18.7071-17.8915.181
20.0919-0.0498-0.11580.085-0.02580.34160.0022-0.0160.01490.01180.0116-0.0062-0.02650.0008-0.01380.00630.0007-0.00350.048-0.00380.0079-1.6854-17.17929.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 172
2X-RAY DIFFRACTION2B6 - 172

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