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- PDB-2eav: Crystal structure of the C-terminal peptidoglycan-binding domain ... -

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Basic information

Entry
Database: PDB / ID: 2eav
TitleCrystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ibeta
ComponentsPeptidoglycan recognition protein-I-beta
KeywordsSUGAR BINDING PROTEIN / ALPHA/BETA MIX
Function / homology
Function and homology information


peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / Antimicrobial peptides / 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 ...peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / Antimicrobial peptides / 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 4 / Peptidoglycan recognition protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCho, S. / Mariuzza, R.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins
Authors: Cho, S. / Wang, Q. / Swaminathan, C.P. / Hesek, D. / Lee, M. / Boons, G.J. / Mobashery, S. / Mariuzza, R.A.
History
DepositionFeb 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 20, 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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-beta
B: Peptidoglycan recognition protein-I-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3398
Polymers35,9872
Non-polymers3526
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-58 kcal/mol
Surface area13880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.435, 56.785, 36.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-67-

HOH

21B-107-

HOH

31B-129-

HOH

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Components

#1: Protein Peptidoglycan recognition protein-I-beta


Mass: 17993.557 Da / Num. of mol.: 2 / Fragment: peptidoglycan-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGRPIB / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q3B822, UniProt: Q96LB8*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.85 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M NiSO4, 15%(w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 23, 2006 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13022 / Num. obs: 12369 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.4 / % possible all: 71.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 670 -RANDOM
Rwork0.229 ---
all0.234 13022 --
obs0.231 12352 91.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 6 139 2663
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.364 --
Rwork0.316 --
obs-704 71.5 %

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