3EP1 | pdb_00003ep1

Structure of the PGRP-Hd from Alvinella pompejana

• PDB DOI: https://doi.org/10.2210/pdb3EP1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Alvinella pompejana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-29 Released: 2009-09-29 
• Deposition Author(s): Delfosse, V., Gagniere, N., Perrodou, E., Poch, O., Lecompte, O., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.302 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Structure of the PGRP-Hd from Alvinella pompejana

Delfosse, V., Gagniere, N., Perrodou, E., Poch, O., Lecompte, O., Mayer, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.5 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 331 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PGRP-Hd - Peptidoglycan recognition protein homologue	A, B	176	Alvinella pompejana	Mutation(s): 0  Gene Names: PGRP-Hd
UniProt
Find proteins for D0VX04 (Alvinella pompejana) Explore D0VX04  Go to UniProtKB:  D0VX04

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.302 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.36	α = 90
b = 71.85	β = 90
c = 141.88	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Delfosse, V., Gagniere, N., Perrodou, E., Poch, O., Lecompte, O., Mayer, C.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary