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- PDB-1sk3: Crystal structure of the C-terminal peptidoglycan-binding domain ... -

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Basic information

Entry
Database: PDB / ID: 1sk3
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 / peptidoglycan binding / biological process involved in interaction with host / 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 / peptidoglycan binding / biological process involved in interaction with host / 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
NICKEL (II) ION / Peptidoglycan recognition protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,4854
Polymers18,2721
Non-polymers2133
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.632, 102.632, 41.496
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18271.795 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG-MME 2000, nickleous sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2003
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 6416 / Num. obs: 6416 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.131
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.505 / Num. unique all: 627 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.63 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1047715.81 / 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
Rfree0.253 346 5.4 %RANDOM
Rwork0.219 ---
all0.219 6405 --
obs0.219 6405 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5311 Å2 / ksol: 0.360846 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å27.23 Å20 Å2
2--2.35 Å20 Å2
3----4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 7 11 1304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.8→2.98 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.329 1042 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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