3CJD | pdb_00003cjd

Crystal structure of putative TetR transcriptional regulator (YP_510936.1) from Jannaschia sp. CCS1 at 1.79 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CJD/pdb

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


• Deposited: 2008-03-12 Released: 2008-04-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of putative TetR transcriptional regulator (YP_510936.1) from Jannaschia sp. CCS1 at 1.79 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.78 kDa 
• Atom Count: 3,122 
• Modeled Residue Count: 364 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B	198	Jannaschia sp. CCS1	Mutation(s): 0  Gene Names: YP_510936.1, Jann_2994

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE	D [auth A], E [auth A]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
CL	C [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CJD

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.283	α = 99.23
b = 46.044	β = 100.39
c = 60.761	γ = 104.79

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary