3L09 | pdb_00003l09

Crystal structure of Putative transcriptional regulator (JANN_22DEC04_CONTIG27_REVISED_GENE3569) from Jannaschia sp. CCS1 at 2.81 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L09/pdb

• Classification: Transcription regulator
• Organism(s): Jannaschia sp. CCS1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-09 Released: 2010-01-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.245 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of Putative transcriptional regulator (JANN_22DEC04_CONTIG27_REVISED_GENE3569) from Jannaschia sp. CCS1 at 2.81 A resolution

Joint Center for Structural Genomics (JCSG)

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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.46 kDa 
• Atom Count: 7,745 
• Modeled Residue Count: 1,005 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B, C, D	266	Jannaschia sp. CCS1	Mutation(s): 0  Gene Names: Jann_0659
UniProt
Find proteins for A0ACD6B873 (Jannaschia sp. (strain CCS1)) Explore A0ACD6B873  Go to UniProtKB:  A0ACD6B873

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth C], I [auth C], J [auth C], K [auth C], L [auth D], M [auth D], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.81 Å
• R-Value Free:  0.245 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33L09

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.953	α = 90
b = 81.722	β = 90
c = 199.921	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
SHELX	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary