2V9D | pdb_00002v9d

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/pdb2V9D/pdb

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

Deposited: 2007-08-23 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: 2.15 Å
R-Value Free:
0.218 (Depositor), 0.216 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 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 Related Structures:
2V8Z, 2V9D, 4PTN

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 148.99 kDa
Atom Count: 9,660
Modeled Residue Count: 1,192
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75682
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.218 (Depositor), 0.216 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.279	α = 90
b = 149.806	β = 108.42
c = 78.967	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-11-06
Changes: Data collection, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary