PDB-9azh: Native nnhA in P1

ID or keywords:

Entry

Database: PDB / ID: 9azh

Title

Native nnhA in P1

Components

2-nitroimidazole nitrohydrolase

Keywords

HYDROLASE / antibacterial / GME superfamily

Function / homology

2-nitroimidazole nitrohydrolase / nitroimidazole catabolic process / arginine deiminase activity / L-arginine deiminase pathway / Arginine deiminase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / response to antibiotic / 2-nitroimidazole nitrohydrolase

Function and homology information

Biological species

Mycobacterium sp. JS330 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Peat, T.S. / Newman, J.

Funding support

Australia, 1items

Citation

Journal: Commun Biol / Year: 2024
Title: Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).
Authors: Ahmed, F.H. / Liu, J.W. / Royan, S. / Warden, A.C. / Esquirol, L. / Pandey, G. / Newman, J. / Scott, C. / Peat, T.S.

History

Deposition	Mar 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9azh.cif.gz	489.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9azh.ent.gz	383.9 KB	Display	PDB format
PDBx/mmJSON format	9azh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9azh_validation.pdf.gz	467.1 KB	Display	wwPDB validaton report
Full document	9azh_full_validation.pdf.gz	476.4 KB	Display
Data in XML	9azh_validation.xml.gz	106.5 KB	Display
Data in CIF	9azh_validation.cif.gz	146.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/9azh ftp://data.pdbj.org/pub/pdb/validation_reports/az/9azh	HTTPS FTP

-
Related structure data

Related structure data	9azgC 9b01C 9b02C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2-nitroimidazole nitrohydrolase

B: 2-nitroimidazole nitrohydrolase

C: 2-nitroimidazole nitrohydrolase

D: 2-nitroimidazole nitrohydrolase

E: 2-nitroimidazole nitrohydrolase

F: 2-nitroimidazole nitrohydrolase

hetero molecules

259 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.727, 117.377, 121.125
Angle α, β, γ (deg.)	117.139, 91.298, 101.377
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 379 / Label seq-ID: 18 - 386

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	2-nitroimidazole nitrohydrolase / 2NI nitrohydrolase Mass: 43132.492 Da / Num. of mol.: 6 / Mutation: T2I, G14D, K73R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium sp. JS330 (bacteria) / Gene: nnhA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: F4ZCI3, 2-nitroimidazole nitrohydrolase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1733 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: Protein at 7mg/mL was set up in SD2 sitting drop plates with 300 nL protein and 150 nL reservoir at 20 C. Reservoir consisted of 21% polyacrylic acid 5100, 20 mM MgCl2 and 100 mM HEPES at pH 7.2

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.18157 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.18157 Å / Relative weight: 1
Reflection	Resolution: 2.04→60.74 Å / Num. obs: 177958 / % possible obs: 98.2 % / Redundancy: 7 % / CC_1/2: 0.987 / R_merge(I) obs: 0.222 / R_pim(I) all: 0.09 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.04→2.07 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.843 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8535 / CC_1/2: 0.696 / R_pim(I) all: 0.39 / % possible all: 94.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.04→54.09 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.942 / SU B: 3.505 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1785	8601	4.841 %
R_work	0.1559	169055	-
all	0.157	-	-
obs	-	177656	98.02 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.886 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.884 Å²	-0.515 Å²	-0.166 Å²
2-	-	-0.726 Å²	-0.338 Å²
3-	-	-	-0.286 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→54.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17346	0	29	1733	19108

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	18110
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	16588
X-RAY DIFFRACTION	r_angle_refined_deg	1.546	1.816	24700
X-RAY DIFFRACTION	r_angle_other_deg	0.531	1.757	38187
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.412	5	2270
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.724	5	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.742	10	2829
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.716	10	891
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2638
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	22222
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4330
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	3308
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	15309
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	8966
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	9100
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	1383
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.103	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.155	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	36
X-RAY DIFFRACTION	r_mcbond_it	1.253	1.321	9002
X-RAY DIFFRACTION	r_mcbond_other	1.252	1.321	9002
X-RAY DIFFRACTION	r_mcangle_it	1.92	2.367	11292
X-RAY DIFFRACTION	r_mcangle_other	1.92	2.367	11293
X-RAY DIFFRACTION	r_scbond_it	2.336	1.615	9108
X-RAY DIFFRACTION	r_scbond_other	2.336	1.616	9109
X-RAY DIFFRACTION	r_scangle_it	3.718	2.827	13406
X-RAY DIFFRACTION	r_scangle_other	3.718	2.827	13407
X-RAY DIFFRACTION	r_lrange_it	5.258	17.194	78315
X-RAY DIFFRACTION	r_lrange_other	5.258	17.194	78316
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.055	0.05	12338
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.049	0.05	12484
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.052	0.05	12427
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.052	0.05	12429
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.056	0.05	12455
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.048	0.05	12276
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.043	0.05	12325
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.038	0.05	12320
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.042	0.05	12267
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.045	0.05	12569
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.046	0.05	12506
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.05	0.05	12516
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.038	0.05	12439
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.041	0.05	12469
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.042	0.05	12336

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05469	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.05469	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04917	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04917	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05153	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05153	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.05182	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.05182	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05611	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05611	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.04771	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.04771	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.04287	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.04287	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.03834	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.03834	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.04196	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.04196	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.04478	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.04478	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.04569	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.04569	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.04973	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.04973	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.03795	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.03795	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.04069	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.04069	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.04212	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.04212	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.04-2.093	0.278	610	0.245	12124	0.247	13374	0.947	0.959	95.2146	0.237
2.093-2.15	0.219	657	0.206	12068	0.206	13099	0.967	0.971	97.1448	0.193
2.15-2.212	0.224	594	0.192	11792	0.194	12735	0.969	0.976	97.2595	0.179
2.212-2.28	0.208	562	0.178	11432	0.179	12287	0.971	0.979	97.6154	0.164
2.28-2.355	0.185	558	0.165	11093	0.166	11933	0.978	0.982	97.6368	0.15
2.355-2.438	0.184	543	0.16	10764	0.161	11556	0.979	0.984	97.8453	0.146
2.438-2.529	0.191	578	0.156	10357	0.158	11164	0.977	0.985	97.9488	0.142
2.529-2.632	0.193	530	0.159	10007	0.161	10741	0.976	0.984	98.1007	0.145
2.632-2.749	0.186	528	0.156	9598	0.157	10306	0.979	0.985	98.2534	0.143
2.749-2.883	0.165	515	0.149	9154	0.15	9817	0.983	0.986	98.4924	0.137
2.883-3.038	0.173	398	0.153	8829	0.154	9367	0.981	0.986	98.5054	0.142
3.038-3.222	0.189	379	0.158	8355	0.159	8855	0.978	0.986	98.6335	0.148
3.222-3.444	0.177	383	0.152	7844	0.153	8323	0.982	0.987	98.8466	0.143
3.444-3.718	0.151	381	0.141	7329	0.142	7787	0.987	0.99	99.0112	0.135
3.718-4.071	0.141	305	0.126	6736	0.127	7104	0.989	0.991	99.1132	0.122
4.071-4.549	0.137	338	0.113	6065	0.114	6454	0.989	0.993	99.2098	0.112
4.549-5.246	0.154	251	0.128	5408	0.129	5696	0.99	0.993	99.3504	0.129
5.246-6.41	0.153	185	0.143	4587	0.143	4793	0.988	0.991	99.5619	0.141
6.41-9.002	0.142	175	0.136	3557	0.137	3749	0.99	0.99	99.5465	0.136
9.002-54.09	0.17	131	0.165	1956	0.165	2097	0.986	0.984	99.5231	0.181

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi