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- PDB-1sk4: crystal structure of the C-terminal peptidoglycan-binding domain ... -

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Basic information

Entry
Database: PDB / ID: 1sk4
Titlecrystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha
ComponentsPeptidoglycan recognition protein I-alpha
KeywordsIMMUNE SYSTEM / alpha/beta mix
Function / homology
Function and homology information


negative regulation of natural killer cell differentiation involved in immune response / peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / biological process involved in interaction with host / peptidoglycan binding / Antimicrobial peptides / negative regulation of type II interferon production / detection of bacterium / peptidoglycan catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide ...negative regulation of natural killer cell differentiation involved in immune response / peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / biological process involved in interaction with host / peptidoglycan binding / Antimicrobial peptides / negative regulation of type II interferon production / detection of bacterium / peptidoglycan catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-positive bacterium / protein heterodimerization activity / innate immune response / protein-containing complex / zinc ion binding / extracellular region / membrane
Similarity search - Function
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGuan, R. / Malchiodi, E.L. / Qian, W. / Schuck, P. / Mariuzza, R.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha
Authors: Guan, R. / Malchiodi, E.L. / Qian, W. / Schuck, P. / Mariuzza, R.A.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan recognition protein I-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1092
Polymers18,0861
Non-polymers231
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Peptidoglycan recognition protein I-alpha
hetero molecules

A: Peptidoglycan recognition protein I-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2174
Polymers36,1712
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4220 Å2
ΔGint-56 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.464, 64.464, 63.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-55-

HOH

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Components

#1: Protein Peptidoglycan recognition protein I-alpha / Peptidoglycan recognition protein intermediate alpha / PGRP-I-alpha / PGLYRPIalpha


Mass: 18085.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGRPIA / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q96LB9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.15 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium potassium tartrate, Zinc chloride, Tritox x-100, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2003
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 18925 / Num. obs: 18925 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.5 / Num. unique all: 1837 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHT

1oht


Resolution: 1.65→28.79 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1237895.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 753 4 %RANDOM
Rwork0.196 ---
all0.196 18900 --
obs0.196 18900 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9213 Å2 / ksol: 0.357945 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å2-0.84 Å20 Å2
2---2.46 Å20 Å2
3---4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.65→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 1 137 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 138 4.5 %
Rwork0.236 2934 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_OCYS_REP.PARAMPROTEIN_OCYS.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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