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- PDB-3ep1: Structure of the PGRP-Hd from Alvinella pompejana -

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Basic information

Entry
Database: PDB / ID: 3ep1
TitleStructure of the PGRP-Hd from Alvinella pompejana
ComponentsPGRP-Hd - Peptidoglycan recognition protein homologue
KeywordsIMMUNE SYSTEM / PGRP-Hd / Alvinella pompejana / thermophile / model system
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding
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 / 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
PGRP-Hd - Peptidoglycan recognition protein homologue
Similarity search - Component
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDelfosse, V. / Gagniere, N. / Perrodou, E. / Poch, O. / Lecompte, O. / Mayer, C.
CitationJournal: To be Published
Title: Structure of the PGRP-Hd from Alvinella pompejana
Authors: Delfosse, V. / Gagniere, N. / Perrodou, E. / Poch, O. / Lecompte, O. / Mayer, C.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PGRP-Hd - Peptidoglycan recognition protein homologue
B: PGRP-Hd - Peptidoglycan recognition protein homologue


Theoretical massNumber of molelcules
Total (without water)38,5032
Polymers38,5032
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-9.1 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.360, 71.850, 141.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PGRP-Hd - Peptidoglycan recognition protein homologue


Mass: 19251.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alvinella pompejana (invertebrata) / Gene: PGRP-Hd / Plasmid details: pHGW is based on the pET22b vector / Plasmid: pHGW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: PDB-3EPI, UniProt: D0VX04*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 200mM Sodium Tartrate, 20% PEG3350, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→29 Å / Num. obs: 21905 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.26 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 4084 / Rsym value: 0.37 / % possible all: 96.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCK

1yck


Resolution: 2.1→28.96 Å / Isotropic thermal model: Restrained / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1096 -Random
Rwork0.247 ---
obs0.247 21905 100 %-
all-21905 --
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--5.35 Å20 Å2
3----3.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 0 233 2696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.359 179 -
Rwork0.296 --
obs-3398 100 %

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