2QL3 | pdb_00002ql3

Crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

The crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1.

Tan, K., Skarina, T., Kagen, O., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 282.47 kDa 
  • Atom Count: 20,701 
  • Modeled Residue Count: 2,460 
  • Deposited Residue Count: 2,508 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable transcriptional regulator, LysR family protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
209Rhodococcus jostii RHA1Mutation(s): 5 
Gene Names: RHA1_ro01847
UniProt
Find proteins for Q0SFM8 (Rhodococcus jostii (strain RHA1))
Explore Q0SFM8 
Go to UniProtKB:  Q0SFM8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0SFM8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4


Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth G]
AC [auth K]
BA [auth C]
BB [auth G]
AA [auth C],
AB [auth G],
AC [auth K],
BA [auth C],
BB [auth G],
BC [auth K],
CA [auth C],
CB [auth H],
CC [auth K],
DA [auth D],
DB [auth H],
DC [auth K],
EA [auth D],
EB [auth H],
EC [auth L],
FA [auth D],
FB [auth H],
FC [auth L],
GA [auth D],
GB [auth I],
GC [auth L],
HA [auth D],
HB [auth I],
HC [auth L],
IA [auth E],
IB [auth I],
IC [auth L],
JA [auth E],
JB [auth I],
JC [auth L],
KA [auth E],
KB [auth I],
LA [auth F],
LB [auth I],
M [auth A],
MA [auth F],
MB [auth I],
N [auth A],
NA [auth F],
NB [auth J],
O [auth A],
OA [auth F],
OB [auth J],
P [auth A],
PA [auth F],
PB [auth J],
Q [auth A],
QA [auth F],
QB [auth J],
R [auth A],
RA [auth F],
RB [auth J],
S [auth B],
SA [auth F],
SB [auth J],
T [auth B],
TA [auth F],
TB [auth J],
U [auth B],
UA [auth F],
UB [auth K],
V [auth B],
VA [auth F],
VB [auth K],
W [auth B],
WA [auth F],
WB [auth K],
X [auth C],
XA [auth F],
XB [auth K],
Y [auth C],
YA [auth F],
YB [auth K],
Z [auth C],
ZA [auth G],
ZB [auth K]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.277α = 90
b = 114.277β = 90
c = 175.359γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary