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- PDB-9azg: Native nnhA in H32 -

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Basic information

Entry
Database: PDB / ID: 9azg
TitleNative nnhA in H32
Components2-nitroimidazole nitrohydrolase
KeywordsHYDROLASE / antibacterial / GME superfamily
Function / homology
Function and homology information


2-nitroimidazole nitrohydrolase / nitroimidazole catabolic process / arginine deiminase activity / L-arginine deiminase pathway / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / response to antibiotic
Similarity search - Function
DI(HYDROXYETHYL)ETHER / 2-nitroimidazole nitrohydrolase
Similarity search - Component
Biological speciesMycobacterium sp. JS330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.162 Å
AuthorsPeat, T.S. / Newman, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: 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
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-nitroimidazole nitrohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3684
Polymers43,1321
Non-polymers2353
Water3,675204
1
A: 2-nitroimidazole nitrohydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)260,20624
Polymers258,7956
Non-polymers1,41118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_557y,x,-z+21
crystal symmetry operation5_557x-y,-y,-z+21
crystal symmetry operation6_557-x,-x+y,-z+21
Buried area32220 Å2
ΔGint-195 kcal/mol
Surface area67730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.360, 206.360, 70.303
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

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Components

#1: Protein 2-nitroimidazole nitrohydrolase / 2NI nitrohydrolase


Mass: 43132.492 Da / Num. of mol.: 1 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Protein at 7mg/mL was set up in sitting drops with 300 nL of protein and 150 nL reservoir. The reservoir solution consisted of 21% polyacrylic acid 5100, 20 mM MgCl2 and 100 mM HEPES pH 7.2 at 20 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45861 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45861 Å / Relative weight: 1
ReflectionResolution: 2.16→48.71 Å / Num. obs: 30547 / % possible obs: 99.9 % / Redundancy: 59.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.02 / Net I/σ(I): 28.1
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2620 / CC1/2: 0.973 / Rpim(I) all: 0.165 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.162→48.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.68 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2065 1504 4.928 %
Rwork0.1677 29015 -
all0.17 --
obs-30519 99.752 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.591 Å2
Baniso -1Baniso -2Baniso -3
1--4.085 Å2-2.042 Å20 Å2
2---4.085 Å20 Å2
3---13.251 Å2
Refinement stepCycle: LAST / Resolution: 2.162→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 15 204 3110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123007
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162762
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.8174092
X-RAY DIFFRACTIONr_angle_other_deg0.5421.7546359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.546522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57910469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.02910147
X-RAY DIFFRACTIONr_chiral_restr0.0740.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
X-RAY DIFFRACTIONr_nbd_refined0.2120.2589
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22612
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.215
X-RAY DIFFRACTIONr_nbd_other0.1620.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.237
X-RAY DIFFRACTIONr_mcbond_it2.1242.9811490
X-RAY DIFFRACTIONr_mcbond_other2.1142.981490
X-RAY DIFFRACTIONr_mcangle_it3.1455.351866
X-RAY DIFFRACTIONr_mcangle_other3.1485.3511867
X-RAY DIFFRACTIONr_scbond_it3.1163.3071517
X-RAY DIFFRACTIONr_scbond_other3.1153.3081518
X-RAY DIFFRACTIONr_scangle_it4.8175.9172226
X-RAY DIFFRACTIONr_scangle_other4.8155.9182227
X-RAY DIFFRACTIONr_lrange_it6.3337.35312925
X-RAY DIFFRACTIONr_lrange_other6.32337.21912829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.162-2.2180.2841060.2952108X-RAY DIFFRACTION98.0514
2.218-2.2790.2851010.2652081X-RAY DIFFRACTION99.9542
2.279-2.3450.2771060.2322029X-RAY DIFFRACTION100
2.345-2.4170.2481000.2221974X-RAY DIFFRACTION100
2.417-2.4960.2751010.1961892X-RAY DIFFRACTION100
2.496-2.5830.2351010.1771838X-RAY DIFFRACTION99.8455
2.583-2.6810.255850.1771790X-RAY DIFFRACTION100
2.681-2.790.204960.1621695X-RAY DIFFRACTION99.9442
2.79-2.9130.211960.1631642X-RAY DIFFRACTION99.8851
2.913-3.0550.226910.171561X-RAY DIFFRACTION99.7585
3.055-3.220.2720.171497X-RAY DIFFRACTION99.8092
3.22-3.4140.202730.181411X-RAY DIFFRACTION99.7982
3.414-3.6480.234740.1751329X-RAY DIFFRACTION99.8577
3.648-3.9390.209510.151256X-RAY DIFFRACTION99.771
3.939-4.3120.172640.1221149X-RAY DIFFRACTION99.8354
4.312-4.8160.11580.1021033X-RAY DIFFRACTION99.9084
4.816-5.5520.155390.118951X-RAY DIFFRACTION100
5.552-6.7780.177450.139780X-RAY DIFFRACTION100
6.778-9.4950.204240.127630X-RAY DIFFRACTION100
9.495-48.710.106210.148369X-RAY DIFFRACTION100

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