1ZEL | pdb_00001zel

Crystal structure of RV2827C protein from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis.

Janowski, R.Panjikar, S.Eddine, A.N.Kaufmann, S.H.Weiss, M.S.

(2009) J Struct Funct Genomics 10: 137-150

  • DOI: https://doi.org/10.1007/s10969-009-9060-4
  • Primary Citation Related Structures: 
    1ZEL

  • PubMed Abstract: 

    Tuberculosis (TB) is a major global health threat caused by Mycobacterium tuberculosis (Mtb). It is further fueled by the HIV pandemic and by increasing incidences of multidrug resistant Mtb-strains. Rv2827c, a hypothetical protein from Mtb, has been implicated in the survival of Mtb in the macrophages of the host. The three-dimensional structure of Rv2827c has been determined by the three-wavelength anomalous diffraction technique using bromide-derivatized crystals and refined to a resolution of 1.93 A. The asymmetric unit of the orthorhombic crystals contains two independent protein molecules related by a non-crystallographic translation. The tertiary structure of Rv2827c comprises two domains: an N-terminal domain displaying a winged helix topology and a C-terminal domain, which appears to constitute a new and unique fold. Based on structural homology considerations and additional biochemical evidence, it could be established that Rv2827c is a DNA-binding protein. Once the understanding of the structure-function relationship of Rv2827c extends to the function of Rv2827c in vivo, new clues for the rational design of novel intervention strategies may be obtained.


  • Organizational Affiliation
    • EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 66.2 kDa 
  • Atom Count: 5,021 
  • Modeled Residue Count: 588 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hypothetical protein Rv2827c
A, B
298Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv2827c
UniProt
Find proteins for Q7D6H9 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore Q7D6H9 
Go to UniProtKB:  Q7D6H9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7D6H9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
O [auth B],
P [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.419α = 90
b = 180.653β = 90
c = 35.112γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations