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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.161 (Depositor), 0.165 (DCC)
R-Value Work:
0.128 (Depositor), 0.133 (DCC)
R-Value Observed:
0.129 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6Q234
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
UNL Query on UNL Download:Ideal Coordinates CCD File	J [auth A], K [auth A]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.161 (Depositor), 0.165 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

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