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- PDB-9b02: nnhA C357A catalytic mutant in tris buffer -

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Basic information

Entry
Database: PDB / ID: 9b02
TitlennhA C357A catalytic mutant in tris buffer
Components2-nitroimidazole nitrohydrolase
KeywordsHYDROLASE / antibacterial / GME superfamily
Function / homology2-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 speciesMycobacterium sp. JS330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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)43,4537
Polymers43,1001
Non-polymers3536
Water6,593366
1
A: 2-nitroimidazole nitrohydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)260,71942
Polymers258,6036
Non-polymers2,11736
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_559y,x,-z+41
crystal symmetry operation5_679x-y+1,-y+2,-z+41
crystal symmetry operation6_769-x+2,-x+y+1,-z+41
Buried area9560 Å2
ΔGint-104 kcal/mol
Surface area91760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.091, 206.091, 69.310
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-402-

NA

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43100.430 Da / Num. of mol.: 1 / Mutation: T2I, G14D, K73R, C357A
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

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Non-polymers , 6 types, 372 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Protein was at 2.5 mg/mL in tris pH 7.0 buffer. The drops were 200 nL plus 200 nL and incubated at 20 C. The reservoir was 21.7% polyacrylic acid 5100, 15 mM MgCl2 and 100 mM HEPES pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.97→40.3 Å / Num. obs: 39795 / % possible obs: 99.8 % / Redundancy: 11.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.055 / Net I/σ(I): 10.9
Reflection shellResolution: 1.97→2.01 Å / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2711 / CC1/2: 0.862 / Rpim(I) all: 0.289

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.661 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1979 2086 5.243 %
Rwork0.1648 37701 -
all0.167 --
obs-39787 99.814 %
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: 18.616 Å2
Baniso -1Baniso -2Baniso -3
1--2.035 Å2-1.017 Å20 Å2
2---2.035 Å20 Å2
3---6.601 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 20 366 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123018
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162770
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.6574110
X-RAY DIFFRACTIONr_angle_other_deg0.5051.5786373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.346522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29110468
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.94210149
X-RAY DIFFRACTIONr_chiral_restr0.0720.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
X-RAY DIFFRACTIONr_nbd_refined0.2060.2599
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22597
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21490
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.213
X-RAY DIFFRACTIONr_nbd_other0.1590.2144
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.266
X-RAY DIFFRACTIONr_mcbond_it1.3071.8681495
X-RAY DIFFRACTIONr_mcbond_other1.2911.8671495
X-RAY DIFFRACTIONr_mcangle_it1.9443.3561874
X-RAY DIFFRACTIONr_mcangle_other1.9473.3581875
X-RAY DIFFRACTIONr_scbond_it2.3042.1481523
X-RAY DIFFRACTIONr_scbond_other2.3032.1521524
X-RAY DIFFRACTIONr_scangle_it3.5783.8122236
X-RAY DIFFRACTIONr_scangle_other3.5783.8162237
X-RAY DIFFRACTIONr_lrange_it4.9624.00213168
X-RAY DIFFRACTIONr_lrange_other4.95924.00213169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0180.3021530.2932711X-RAY DIFFRACTION97.9145
2.018-2.0730.251480.2632694X-RAY DIFFRACTION100
2.073-2.1330.2661530.2272642X-RAY DIFFRACTION100
2.133-2.1990.2141380.2232559X-RAY DIFFRACTION99.9629
2.199-2.270.1981250.1762469X-RAY DIFFRACTION100
2.27-2.350.2321420.1682371X-RAY DIFFRACTION100
2.35-2.4380.2081510.1672303X-RAY DIFFRACTION100
2.438-2.5370.2151240.1552221X-RAY DIFFRACTION100
2.537-2.650.2311270.1622132X-RAY DIFFRACTION99.9557
2.65-2.7780.1921180.1432048X-RAY DIFFRACTION100
2.778-2.9280.1941050.1381934X-RAY DIFFRACTION100
2.928-3.1050.2011100.1521858X-RAY DIFFRACTION100
3.105-3.3170.208840.1681741X-RAY DIFFRACTION100
3.317-3.5810.206840.1791624X-RAY DIFFRACTION100
3.581-3.920.158750.1451494X-RAY DIFFRACTION100
3.92-4.3780.126730.111366X-RAY DIFFRACTION99.9306
4.378-5.0450.134460.1141226X-RAY DIFFRACTION99.843
5.045-6.1550.172540.1381019X-RAY DIFFRACTION100
6.155-8.6040.172430.134815X-RAY DIFFRACTION100
8.604-40.30.167330.154474X-RAY DIFFRACTION100

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