3BDI | pdb_00003bdi

Crystal structure of predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BDI/pdb

• Classification: HYDROLASE
• Organism(s): Thermoplasma acidophilum DSM 1728
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-14 Released: 2007-11-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.83 kDa 
• Atom Count: 1,938 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Ta0194	A	207	Thermoplasma acidophilum DSM 1728	Mutation(s): 10  Gene Names: NP_393672.1, Ta0194
UniProt
Find proteins for Q9HLN3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HLN3  Go to UniProtKB:  Q9HLN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BDI

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.384	α = 90
b = 46.292	β = 90
c = 101.644	γ = 90

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: 2007-11-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, 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: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary