8C0H

Crystal structure of guanidinase from Nitrospira inopinata

PDB DOI: https://doi.org/10.2210/pdb8C0H/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Candidatus Nitrospira inopinata
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-16 Released: 2023-12-27
Deposition Author(s): Puehringer, D.
Funding Organization(s): Vienna Science and Technology Fund (WWTF), Christian Doppler Forschungsgesellschaft, University of Vienna Research Platform Comammox, European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.214
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Growth of complete ammonia oxidizers on guanidine

Palatinszky, M., Herbold, C.W., Sedlacek, C.J., Puehringer, D., Wasmund, K., Nielsen, P.H., Dueholm, M.S., Jehmlich, N., Grusek, R., Kostan, J., Krasnici, N., Palmetzhofer, J., Hofmann, T., Zumstein, M., Djinovic-Carugo, K., Daims, H., Wagner, M.

To be published.

Macromolecule Content

Total Structure Weight: 504.31 kDa
Atom Count: 37,401
Modelled Residue Count: 4,490
Deposited Residue Count: 4,608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative agmatinase 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	384	Candidatus Nitrospira inopinata	Mutation(s): 0 Gene Names: speB, NITINOP_1173 EC: 3.5.3.11
UniProt
Find proteins for A0A0S4KUT0 (Candidatus Nitrospira inopinata) Explore A0A0S4KUT0 Go to UniProtKB: A0A0S4KUT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S4KUT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CB [auth K] SDF format, chain DB [auth K] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GB [auth L] SDF format, chain HB [auth L] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain UA [auth I] SDF format, chain VA [auth I] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain YA [auth J] SDF format, chain ZA [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth L] MOL2 format, chain HB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain ZA [auth J]	AA [auth D] BA [auth D] CB [auth K] DB [auth K] EA [auth E] AA [auth D], BA [auth D], CB [auth K], DB [auth K], EA [auth E], FA [auth E], GB [auth L], HB [auth L], IA [auth F], JA [auth F], MA [auth G], NA [auth G], O [auth A], P [auth A], QA [auth H], RA [auth H], S [auth B], T [auth B], UA [auth I], VA [auth I], W [auth C], X [auth C], YA [auth J], ZA [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth J] Focus chain ZA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth J] Focus chain ZA [auth J]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EB [auth L] SDF format, chain FB [auth L] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain SA [auth I] SDF format, chain TA [auth I] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain WA [auth J] SDF format, chain XA [auth J] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EB [auth L] MOL2 format, chain FB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth J] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AB [auth K] BB [auth K] CA [auth E] DA [auth E] EB [auth L] AB [auth K], BB [auth K], CA [auth E], DA [auth E], EB [auth L], FB [auth L], GA [auth F], HA [auth F], KA [auth G], LA [auth G], M [auth A], N [auth A], OA [auth H], PA [auth H], Q [auth B], R [auth B], SA [auth I], TA [auth I], U [auth C], V [auth C], WA [auth J], XA [auth J], Y [auth D], Z [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth C] Focus chain V [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth C] Focus chain V [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.214
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.15151/ESRF-ES-771426868

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.965	α = 90
b = 164.791	β = 90.03
c = 143.965	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Puehringer, D.

Funding Organization	Location	Grant Number
Vienna Science and Technology Fund (WWTF)	Austria	FA705009
Christian Doppler Forschungsgesellschaft	Austria	FA743017
University of Vienna Research Platform Comammox	Austria	326300
European Regional Development Fund	European Union	FA263001