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- PDB-5dwf: Crystal structure of the complex of Peptidoglycan recognition pro... -

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Basic information

Entry
Database: PDB / ID: 5dwf
TitleCrystal structure of the complex of Peptidoglycan recognition protein, PGRP-S from camel with ethylene glycol at 1.83 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / PGRP / complex / ethylene glycol
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. / Lysozyme-like / Peptidoglycan recognition protein-like / N-acetylmuramoyl-L-alanine amidase / Ami_2 / 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 / N-acetylmuramoyl-L-alanine amidase / Ami_2 / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsSingh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Peptidoglycan recognition protein, PGRP-S from camel with ethylene glycol at 1.83 A resolution
Authors: Singh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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 1.2Nov 6, 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 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)74,3748
Polymers74,0084
Non-polymers3664
Water4,558253
1
A: Peptidoglycan recognition protein 1


Theoretical massNumber of molelcules
Total (without water)18,5021
Polymers18,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7720 Å2
MethodPISA
2
B: Peptidoglycan recognition protein 1


Theoretical massNumber of molelcules
Total (without water)18,5021
Polymers18,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7770 Å2
MethodPISA
3
C: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7143
Polymers18,5021
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7760 Å2
MethodPISA
4
D: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6563
Polymers18,5021
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-3 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.775, 101.525, 163.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-352-

HOH

21D-345-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 6 - 171 / Label seq-ID: 1 - 166

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 18501.947 Da / Num. of mol.: 4 / Fragment: UNP residues 28-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: PGLYRP1, PGLYRP, PGRP / Production host: Camelus dromedarius (Arabian camel) / References: UniProt: Q9GK12
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350 Sodium potassium tartarate / PH range: 7.0-7.5 / Temp details: k

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 64628 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.06 / Net I/σ(I): 16.4
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPdata processing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o4k

3o4k


Resolution: 1.83→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.017 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1288 2 %RANDOM
Rwork0.273 ---
obs0.274 63338 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---2.58 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 24 253 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195375
X-RAY DIFFRACTIONr_bond_other_d0.0080.024978
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9267311
X-RAY DIFFRACTIONr_angle_other_deg1.418311350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72821.846260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75215804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6991564
X-RAY DIFFRACTIONr_chiral_restr0.0890.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216200
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021388
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_it2.943.1762652
X-RAY DIFFRACTIONr_mcbond_other2.9393.1752651
X-RAY DIFFRACTIONr_mcangle_it4.2564.7483308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98260.09
12B98260.09
21A98900.08
22C98900.08
31A98110.08
32D98110.08
41B98260.09
42C98260.09
51B96820.1
52D96820.1
61C99400.08
62D99400.08
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 103 -
Rwork0.433 4538 -
obs--97.75 %

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