3CNG | pdb_00003cng

Crystal structure of NUDIX hydrolase from Nitrosomonas europaea

PDB DOI: https://doi.org/10.2210/pdb3CNG/pdb

Classification: HYDROLASE
Organism(s): Nitrosomonas europaea ATCC 19718
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-25 Released: 2008-04-08
Deposition Author(s): Osipiuk, J., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.233 (Depositor), 0.270 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structure of NUDIX hydrolase from Nitrosomonas europaea.

Osipiuk, J., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 88.5 kDa
Atom Count: 6,189
Modeled Residue Count: 708
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUDIX hydrolase	A, B, C, D	189	Nitrosomonas europaea ATCC 19718	Mutation(s): 0 Gene Names: NE1158
UniProt
Find proteins for Q82VD6 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82VD6 Go to UniProtKB: Q82VD6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82VD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A]	K [auth A], P [auth B], T [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], Q [auth C], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain J [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain J [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain J [auth A]	J [auth A], S [auth C], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain S [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] N [auth B] O [auth B] G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], R [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233 (Depositor), 0.270 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.781	α = 90
b = 49.506	β = 106.28
c = 110.19	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

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Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-08
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: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary