2NYX | pdb_00002nyx

Crystal structure of RV1404 from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb2NYX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-21 Released: 2006-12-05 
• Deposition Author(s): Yu, M., Bursey, E.H., Radhakannan, R., Kim, C.-Y., Kaviratne, T., Woodruff, T., Segelke, B.W., Lekin, T., Toppani, D., Terwilliger, T.C., Hung, L.-W., TB Structural Genomics Consortium (TBSGC), Integrated Center for Structure and Function Innovation (ISFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of RV1404 from Mycobacterium tuberculosis

Yu, M., Bursey, E.H., Radhakannan, R., Kim, C.-Y., Kaviratne, T., Woodruff, T., Segelke, B.W., Lekin, T., Toppani, D., Terwilliger, T.C., Hung, L.-W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.22 kDa 
• Atom Count: 4,602 
• Modeled Residue Count: 586 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulatory protein, Rv1404	A, B, C, D	168	Mycobacterium tuberculosis H37Rv	Mutation(s): 4  Gene Names: Rv1404
UniProt
Find proteins for P71672 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P71672  Go to UniProtKB:  P71672

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.262	α = 90
b = 54.747	β = 90
c = 227.505	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Yu, M., Bursey, E.H., Radhakannan, R., Kim, C.-Y., Kaviratne, T., Woodruff, T., Segelke, B.W., Lekin, T., Toppani, D., Terwilliger, T.C., Hung, L.-W., TB Structural Genomics Consortium (TBSGC), Integrated Center for Structure and Function Innovation (ISFI)

Revision History  

• Version 1.0: 2006-12-05
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary