4LRV | pdb_00004lrv

Crystal structure of DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

PDB DOI: https://doi.org/10.2210/pdb4LRV/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli B7A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-21 Released: 2013-08-28
Deposition Author(s): Hu, W., Wang, C.K., Liang, J.D., Zhang, T.L., Yang, M., Hu, Z.P., Wang, Z.J., Lan, W.X., Wu, H.M., Ding, J.P., Wu, G., Deng, Z.X., Cao, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor), 0.198 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

Hu, W., Wang, C.K., Liang, J.D., Zhang, T.L., Hu, Z.P., Wang, Z.J., Lan, W.X., Li, F., Wu, H.M., Ding, J.P., Wu, G., Deng, Z.X., Cao, C.

(2012) Cell Res 22: 1203-1206

PubMed: 22525332 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2012.66
Primary Citation Related Structures:
4LRV

Macromolecule Content

Total Structure Weight: 201.19 kDa
Atom Count: 13,759
Modeled Residue Count: 1,675
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA sulfur modification protein DndE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	109	Escherichia coli B7A	Mutation(s): 0 Gene Names: dndE, EcB7A_5348

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.242 (Depositor), 0.237 (DCC)
R-Value Work: 0.201 (Depositor), 0.198 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.845	α = 90
b = 97.306	β = 95.81
c = 218.532	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2013-09-04
Changes: Experimental preparation
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary