3U41
Crystal structure of Escherichia coli DmsD in space group P212121
- PDB DOI: https://doi.org/10.2210/pdb3U41/pdb
- Classification: CHAPERONE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2011-10-06 Released: 2013-02-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.271 
- R-Value Work: 0.230 
- R-Value Observed: 0.232 
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Twin-arginine leader-binding protein dmsD | 207 | Escherichia coli K-12 | Mutation(s): 0  Gene Names: b1591, dmsD, JW5262, ynfI | ||
UniProt | |||||
Find proteins for P69853 (Escherichia coli (strain K12)) Explore P69853  Go to UniProtKB:  P69853 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P69853 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TRS Query on TRS | DA [auth C], U [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
PEG Query on PEG | OA [auth D] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
SO4 Query on SO4 | O [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CL Query on CL | CB [auth F], DB [auth F], EA [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.271 
- R-Value Work: 0.230 
- R-Value Observed: 0.232 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 94.275 | α = 90 |
b = 96.221 | β = 90 |
c = 210.243 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MxDC | data collection |
HKL-2000 | data reduction |
PHASES | phasing |
Entry History 
Deposition Data
- Released Date: 2013-02-06  Deposition Author(s): Stevens, C.M., Paetzel, M.
Revision History (Full details and data files)
- Version 1.0: 2013-02-06
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description