6IDM

Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb6IDM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Camelus dromedarius
Mutation(s): No

Deposited: 2018-09-10 Released: 2018-09-26
Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.265
R-Value Work: 0.192
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution

Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 74.16 kDa
Atom Count: 5,334
Modelled Residue Count: 664
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	166	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12 Go to UniProtKB: Q9GK12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GK12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C]	E [auth C]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.265
R-Value Work: 0.192
R-Value Observed: 0.195
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.309	α = 90
b = 101.149	β = 90
c = 163.566	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.