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- PDB-9uge: Crystal structure of the complex of camel peptidoglycan recogniti... -

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Basic information

Entry
Database: PDB / ID: 9uge
TitleCrystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / PGRP-S / Innate immune protein
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. / N-acetylmuramoyl-L-alanine amidase / Ami_2 / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
D-MALATE / OXALIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsBarik, D. / Ahmad, N. / Maurya, A. / Yamini, S. / Sharma, P. / Yadav, S.P. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Crystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution
Authors: Barik, D. / Ahmad, N. / Maurya, A. / Yamini, S. / Sharma, P. / Yadav, S.P. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 11, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 14, 2025ID: 4Q9E
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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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)76,3607
Polymers76,0464
Non-polymers3143
Water6,684371
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1


Theoretical massNumber of molelcules
Total (without water)38,0232
Polymers38,0232
Non-polymers00
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)38,3375
Polymers38,0232
Non-polymers3143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.308, 101.623, 162.683
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-227-

HOH

21D-322-

HOH

31D-352-

HOH

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Components

#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
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.94 %
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: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.305→40.704 Å / Num. obs: 29076 / % possible obs: 89.2 % / Redundancy: 1 % / Biso Wilson estimate: 44.6 Å2 / Rsym value: 0.074 / Net I/σ(I): 9.8
Reflection shellResolution: 2.305→2.34 Å / Num. unique obs: 797 / Rsym value: 0.668

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data collection
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.305→40.704 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.913 / SU B: 18.219 / SU ML: 0.374 / Cross valid method: FREE R-VALUE / ESU R: 0.534 / ESU R Free: 0.308
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2833 700 2.407 %
Rwork0.2147 28376 -
all0.216 --
obs-29076 88.909 %
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: 55.996 Å2
Baniso -1Baniso -2Baniso -3
1-7.997 Å2-0 Å20 Å2
2---6.24 Å2-0 Å2
3----1.757 Å2
Refinement stepCycle: LAST / Resolution: 2.305→40.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 21 371 5740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165023
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.8047538
X-RAY DIFFRACTIONr_angle_other_deg0.4481.75611492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.118566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84210816
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.91410268
X-RAY DIFFRACTIONr_chiral_restr0.0590.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021408
X-RAY DIFFRACTIONr_nbd_refined0.2110.21400
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.25413
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22726
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2317
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.238
X-RAY DIFFRACTIONr_nbd_other0.210.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.233
X-RAY DIFFRACTIONr_mcbond_it3.4675.8262732
X-RAY DIFFRACTIONr_mcbond_other3.4665.8262732
X-RAY DIFFRACTIONr_mcangle_it5.71810.4493408
X-RAY DIFFRACTIONr_mcangle_other5.71810.4493409
X-RAY DIFFRACTIONr_scbond_it3.5966.2422794
X-RAY DIFFRACTIONr_scbond_other3.5946.2392783
X-RAY DIFFRACTIONr_scangle_it6.00411.3444130
X-RAY DIFFRACTIONr_scangle_other6.00211.344119
X-RAY DIFFRACTIONr_lrange_it10.51363.0026557
X-RAY DIFFRACTIONr_lrange_other10.51263.0156552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.305-2.3650.395560.40919830.40923820.7550.8185.60030.362
2.365-2.4290.369500.38719950.38623090.8350.83188.56650.337
2.429-2.4990.424510.36319580.36522590.8080.85588.93320.313
2.499-2.5760.4430.35719030.35822060.8310.86588.2140.305
2.576-2.660.344460.33318210.33321180.860.8888.14920.276
2.66-2.7530.363480.29717810.29820720.8660.91188.27220.249
2.753-2.8570.379480.27617110.27919990.8570.9387.9940.228
2.857-2.9730.34320.26816540.26919080.9140.93788.36480.231
2.973-3.1040.326440.24615930.24818430.9190.95188.82260.208
3.104-3.2550.277380.21915180.22117610.9240.96488.35890.189
3.255-3.4290.293440.18814690.19216950.9450.97489.26250.167
3.429-3.6360.319270.18514100.18716150.9410.97888.97830.171
3.636-3.8850.208240.18113190.18115030.970.97889.35460.17
3.885-4.1930.298300.15912260.16314000.9570.98389.71430.149
4.193-4.5880.204220.13711520.13812960.9740.98790.58640.134
4.588-5.1220.221260.15210490.15411840.9670.98790.79390.147
5.122-5.8980.192230.1749480.17510610.9770.98391.51740.16
5.898-7.1860.228180.1688190.1699010.9720.98392.89680.162
7.186-10.0080.183200.1426520.1447250.9860.98892.68970.151
10.008-40.7040.281100.1784150.184550.9260.97893.40660.198

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