3V7P | pdb_00003v7p

Crystal structure of amidohydrolase nis_0429 (target efi-500396) from Nitratiruptor sp. sb155-2

• PDB DOI: https://doi.org/10.2210/pdb3V7P/pdb

• Classification: HYDROLASE
• Organism(s): Nitratiruptor sp. SB155-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-21 Released: 2012-01-11 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.161 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Literature

Crystal Structure of Amidohydrolase Nis_0429 (Target Efi-500319) from Nitratiruptor Sp. Sb155-2

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 49.15 kDa 
• Atom Count: 3,589 
• Modeled Residue Count: 409 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase family protein	A	427	Nitratiruptor sp. SB155-2	Mutation(s): 0  Gene Names: NIS_0429 EC: 3.5.4.40
UniProt
Find proteins for A6Q234 (Nitratiruptor sp. (strain SB155-2)) Explore A6Q234  Go to UniProtKB:  A6Q234

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	F [auth A], G [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
BEZ	D [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	H [auth A], I [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
UNL	J [auth A], K [auth A]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.161 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.515	α = 90
b = 75.169	β = 120.72
c = 75.646	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary