2P4Z

A Ferredoxin-like Metallo-beta-lactamase Superfamily Protein from Thermoanaerobacter tengcongensis

• PDB DOI: https://doi.org/10.2210/pdb2P4Z/pdb

• Classification: HYDROLASE
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-14 Released: 2008-03-18 
• Deposition Author(s): Liang, D.-C., Gu, S.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Crystal structure of Tflp: A ferredoxin-like metallo-beta-lactamase superfamily protein from Thermoanaerobacter tengcongensis

Gu, S.-Y., Yan, X.-X., Liang, D.-C.

(2008) Proteins 72: 531-536

• PubMed: 18431751 
• DOI: https://doi.org/10.1002/prot.22069
• Primary Citation of Related Structures:  
  2P4Z

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.75 kDa 
• Atom Count: 4,576 
• Modelled Residue Count: 551 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-dependent hydrolases of the beta-lactamase superfamily II	A, B	284	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0
UniProt
Find proteins for Q8R8V2 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8R8V2  Go to UniProtKB:  Q8R8V2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth A], E [auth B], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.197	α = 90
b = 138.31	β = 90
c = 52.959	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Liang, D.-C., Gu, S.-Y.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary