2DPP | pdb_00002dpp

Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratase

• PDB DOI: https://doi.org/10.2210/pdb2DPP/pdb

• Classification: LYASE
• Organism(s): Bacillus sp. RAPc8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-05-12 Released: 2007-05-22 
• Deposition Author(s): Tsekoa, T.L., Tastan-Bishop, A.O., Cameron, R.A., Sewell, B.T., Sayed, M.F., Cowan, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratse

Tsekoa, T.L., Tastan-Bishop, A.O., Cameron, R.A., Sewell, B.T., Sayed, M.F., Cowan, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.34 kDa 
• Atom Count: 3,692 
• Modeled Residue Count: 429 
• Deposited Residue Count: 445 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase alpha subunit	A	216	Bacillus sp. RAPc8	Mutation(s): 2  EC: 4.2.1.84
UniProt
Find proteins for Q84FS5 (Bacillus sp. RAPc8) Explore Q84FS5  Go to UniProtKB:  Q84FS5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase beta subunit	B	229	Bacillus sp. RAPc8	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for Q84FS6 (Bacillus sp. RAPc8) Explore Q84FS6  Go to UniProtKB:  Q84FS6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.62	α = 90
b = 106.62	β = 90
c = 83.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Tsekoa, T.L., Tastan-Bishop, A.O., Cameron, R.A., Sewell, B.T., Sayed, M.F., Cowan, D.A.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-23
  Changes: Structure summary