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- PDB-7xu8: Structure of the complex of camel peptidoglycan recognition prote... -

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Basic information

Entry
Database: PDB / ID: 7xu8
TitleStructure of the complex of camel peptidoglycan recognition protein-short (PGRP-S) with heptanoic acid at 2.15 A resolution.
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / CPGRP-S / innate immune system
Function / homology
Function and homology information


peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / negative regulation of cytokine production / detection of bacterium / 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
CARBONATE ION / HYDROGEN PEROXIDE / HEPTANOIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMaurya, A. / Ahmad, N. / Viswanathan, V. / Singh, P.K. / Yamini, S. / Sharma, P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: Int J Biochem Mol Biol / Year: 2022
Title: Ligand recognition by peptidoglycan recognition protein-S (PGRP-S): structure of the complex of camel PGRP-S with heptanoic acid at 2.15 angstrom resolution.
Authors: Maurya, A. / Ahmad, N. / Singh, P.K. / Viswanathan, V. / Kaur, P. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 15, 2022ID: 3UML
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
C: Peptidoglycan recognition protein 1
D: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,93221
Polymers76,0464
Non-polymers88617
Water10,971609
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43410
Polymers38,0232
Non-polymers4118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peptidoglycan recognition protein 1
D: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,49711
Polymers38,0232
Non-polymers4749
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.896, 101.637, 163.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-357-

HOH

21D-355-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
22B
33A
44C
55A
66D
77B
88C
99B
1010D
1111C
1212D

NCS domain segments:

Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 6 - 171 / Label seq-ID: 6 - 171

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
222BB
333AA
444CC
555AA
666DD
777BB
888CC
999BB
101010DD
111111CC
121212DD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7
8
9
10
11
12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptidoglycan recognition protein 1 / Peptidoglycan recognition protein short / PGRP-S


Mass: 19011.459 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Camelus dromedarius (Arabian camel) / References: UniProt: Q9GK12

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Non-polymers , 7 types, 626 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SHV / HEPTANOIC ACID


Mass: 130.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 20% glycerol, 6% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2011
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→43.15 Å / Num. obs: 40935 / % possible obs: 99.71 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.95 / Rsym value: 0.0432 / Net I/σ(I): 13.1
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2987 / CC1/2: 0.919 / Rsym value: 0.16 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2X

3c2x


Resolution: 2.15→43.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.99 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.298 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2819 2035 4.971 %
Rwork0.2201 38900 -
all0.223 --
obs-40935 99.708 %
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: 40.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.037 Å20 Å20 Å2
2---0.25 Å2-0 Å2
3---0.213 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 56 609 5869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135413
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174980
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6467355
X-RAY DIFFRACTIONr_angle_other_deg1.2811.57811356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64219.506324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1061564
X-RAY DIFFRACTIONr_chiral_restr0.0680.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021408
X-RAY DIFFRACTIONr_nbd_refined0.2040.21233
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.25156
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22598
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2481
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.28
X-RAY DIFFRACTIONr_metal_ion_refined0.3870.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.232
X-RAY DIFFRACTIONr_nbd_other0.260.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.220
X-RAY DIFFRACTIONr_mcbond_it3.0774.0852665
X-RAY DIFFRACTIONr_mcbond_other3.0754.0852664
X-RAY DIFFRACTIONr_mcangle_it4.5526.123326
X-RAY DIFFRACTIONr_mcangle_other4.5526.1213327
X-RAY DIFFRACTIONr_scbond_it3.3654.452748
X-RAY DIFFRACTIONr_scbond_other3.3654.452749
X-RAY DIFFRACTIONr_scangle_it5.136.5334029
X-RAY DIFFRACTIONr_scangle_other5.1296.5334030
X-RAY DIFFRACTIONr_lrange_it8.0449.4026459
X-RAY DIFFRACTIONr_lrange_other8.0349.4086457
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.055491
X-RAY DIFFRACTIONr_ncsr_local_group_20.080.055504
X-RAY DIFFRACTIONr_ncsr_local_group_30.0830.055481
X-RAY DIFFRACTIONr_ncsr_local_group_40.0720.055502
X-RAY DIFFRACTIONr_ncsr_local_group_50.0750.055503
X-RAY DIFFRACTIONr_ncsr_local_group_60.0730.055551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08950.0501
12BX-RAY DIFFRACTIONLocal ncs0.08950.0501
23AX-RAY DIFFRACTIONLocal ncs0.08040.0501
24CX-RAY DIFFRACTIONLocal ncs0.08040.0501
35AX-RAY DIFFRACTIONLocal ncs0.0830.0501
36DX-RAY DIFFRACTIONLocal ncs0.0830.0501
47BX-RAY DIFFRACTIONLocal ncs0.071870.05009
48CX-RAY DIFFRACTIONLocal ncs0.071870.05009
59BX-RAY DIFFRACTIONLocal ncs0.074590.0501
510DX-RAY DIFFRACTIONLocal ncs0.074590.0501
611CX-RAY DIFFRACTIONLocal ncs0.072750.0501
612DX-RAY DIFFRACTIONLocal ncs0.072750.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.4381210.3962857X-RAY DIFFRACTION99.6987
2.206-2.2660.41480.3452775X-RAY DIFFRACTION99.693
2.266-2.3320.4161310.3432680X-RAY DIFFRACTION99.7516
2.332-2.4030.4411560.3512592X-RAY DIFFRACTION99.6736
2.403-2.4820.3831150.3072559X-RAY DIFFRACTION99.7389
2.482-2.5680.3431590.2962414X-RAY DIFFRACTION99.7673
2.568-2.6650.3371280.2732394X-RAY DIFFRACTION99.8021
2.665-2.7730.3081310.2782253X-RAY DIFFRACTION99.7072
2.773-2.8960.3391250.2542195X-RAY DIFFRACTION99.7849
2.896-3.0370.2771060.2252124X-RAY DIFFRACTION99.9104
3.037-3.20.302890.2252022X-RAY DIFFRACTION99.9053
3.2-3.3930.3291020.2071903X-RAY DIFFRACTION99.6521
3.393-3.6260.2691050.1871772X-RAY DIFFRACTION99.8936
3.626-3.9140.222790.1891696X-RAY DIFFRACTION99.6631
3.914-4.2840.194790.1631547X-RAY DIFFRACTION99.8772
4.284-4.7840.19820.1411403X-RAY DIFFRACTION99.8655
4.784-5.5130.251620.1751252X-RAY DIFFRACTION99.7722
5.513-6.7240.234360.1631099X-RAY DIFFRACTION99.912
6.724-9.3960.231520.146856X-RAY DIFFRACTION99.89
8-100.19290.186507X-RAY DIFFRACTION96.5766

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