2NUJ | pdb_00002nuj

Crystal structure of thioesterase superfamily (YP_509914.1) from Jannaschia Sp. CCS1 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2NUJ/pdb

• Classification: HYDROLASE
• Organism(s): Jannaschia
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-09 Released: 2006-12-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of thioesterase superfamily (YP_509914.1) from Jannaschia Sp. CCS1 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.03 kDa 
• Atom Count: 2,827 
• Modeled Residue Count: 318 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily	A, B	163	Jannaschia	Mutation(s): 4  Gene Names: YP_509914.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

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: 2.00 Å
• R-Value Free:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32NUJ

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.401	α = 90
b = 78.401	β = 90
c = 151.418	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary