2V8Z

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12

PDB DOI: https://doi.org/10.2210/pdb2V8Z/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-16 Released: 2008-03-04
Deposition Author(s): Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Yage, a Putative Dhdps Like Protein from Escherichia Coli K12.

Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

(2008) Proteins 71: 2102

PubMed: 18361457 Search on PubMed
DOI: https://doi.org/10.1002/prot.22023
Primary Citation of Related Structures:
2V8Z, 2V9D, 4PTN

Organizational Affiliation

School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamilnadu, India.

Macromolecule Content

Total Structure Weight: 148.05 kDa
Atom Count: 9,478
Modelled Residue Count: 1,192
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YAGE	A, B, C, D	343	Escherichia coli K-12	Mutation(s): 0 EC: 4.1.2.51 (UniProt), 4.1.2.28 (UniProt)
UniProt
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682 Go to UniProtKB: P75682
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75682
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.689	α = 90
b = 156.494	β = 90
c = 55.884	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Greenblatt, H.M.

Krishnaswamy, S.

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Refinement description, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Other, 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 R01GM157729.