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
Deposition Author(s): Stevens, C.M., Paetzel, M.

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

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 193.59 kDa
Atom Count: 13,942
Modelled Residue Count: 1,630
Deposited Residue Count: 1,656
Unique protein chains: 1

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	A, B, C, D, E A, B, C, D, E, F, G, H	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain U [auth B]	DA [auth C], U [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain DA [auth C] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain OA [auth D] MOL2 format, chain OA [auth D]	OA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain OA [auth D] Interactions & Density Focus chain OA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain WA [auth E] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain Z [auth C] SDF format, chain ZA [auth F] SDF format, chain EB [auth H] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain V [auth C] SDF format, chain VA [auth E] SDF format, chain XA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain EB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth E] MOL2 format, chain XA [auth F]	AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth C], AB [auth F], BA [auth C], BB [auth F], CA [auth C], EB [auth H], FA [auth D], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], P [auth B], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], UA [auth E], V [auth C], VA [auth E], W [auth C], WA [auth E], X [auth C], XA [auth F], Y [auth C], YA [auth F], Z [auth C], ZA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth C] Focus chain VA [auth E] Focus chain W [auth C] Focus chain WA [auth E] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth C] Focus chain VA [auth E] Focus chain W [auth C] Focus chain WA [auth E] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain EA [auth C] SDF format, chain DB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain DB [auth F]	CB [auth F], DB [auth F], EA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth C] Interactions & Density Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth C]

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 Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
HKL-2000	data reduction
PHASES	phasing

Structure Validation

View Full Validation Report

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