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- PDB-9b01: Catalytic mutant C357A nnhA in CHES buffer -

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Basic information

Entry
Database: PDB / ID: 9b01
TitleCatalytic mutant C357A nnhA in CHES buffer
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
FORMIC ACID / 2-nitroimidazole nitrohydrolase
Similarity search - Component
Biological speciesMycobacterium sp. JS330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)43,3647
Polymers43,1001
Non-polymers2646
Water7,458414
1
A: 2-nitroimidazole nitrohydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)260,18742
Polymers258,6036
Non-polymers1,58436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_649y+1,x-1,-z+41
crystal symmetry operation5_559x-y,-y,-z+41
crystal symmetry operation6_769-x+2,-x+y+1,-z+41
Buried area8950 Å2
ΔGint-141 kcal/mol
Surface area91120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.124, 206.124, 68.215
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-401-

NA

21A-865-

HOH

31A-914-

HOH

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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 , 5 types, 420 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Protein was at 2.5 mg/mL in CHES buffer at pH 9.0 and was set up in 200 nL plus 200 nL drops at 20 C. The reservoir was 21.2% polyacrylic acid 5100, 30 mM MgCl2 and 100 mM HEPES at 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: 1.99→48 Å / Num. obs: 37832 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.072 / Net I/σ(I): 9.7
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2570 / CC1/2: 0.83 / Rpim(I) all: 0.322 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.324 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1738 1967 5.199 %
Rwork0.146 35865 -
all0.147 --
obs-37832 99.834 %
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: 14.262 Å2
Baniso -1Baniso -2Baniso -3
1--1.159 Å2-0.58 Å20 Å2
2---1.159 Å20 Å2
3---3.76 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 14 414 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123013
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162764
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.8174104
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7586357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.198523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60210468
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.92710149
X-RAY DIFFRACTIONr_chiral_restr0.0810.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.2150.2579
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22631
X-RAY DIFFRACTIONr_nbtor_refined0.180.21498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.28
X-RAY DIFFRACTIONr_nbd_other0.1640.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.259
X-RAY DIFFRACTIONr_mcbond_it1.041.4111495
X-RAY DIFFRACTIONr_mcbond_other1.041.4121496
X-RAY DIFFRACTIONr_mcangle_it1.5892.531874
X-RAY DIFFRACTIONr_mcangle_other1.5912.5311875
X-RAY DIFFRACTIONr_scbond_it2.1891.6491518
X-RAY DIFFRACTIONr_scbond_other2.191.6471517
X-RAY DIFFRACTIONr_scangle_it3.3842.9192230
X-RAY DIFFRACTIONr_scangle_other3.3842.922231
X-RAY DIFFRACTIONr_lrange_it4.79918.24913367
X-RAY DIFFRACTIONr_lrange_other4.79918.24913368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.0420.2521270.2252583X-RAY DIFFRACTION98.2952
2.042-2.0970.2321560.1972551X-RAY DIFFRACTION100
2.097-2.1580.2121290.1792512X-RAY DIFFRACTION100
2.158-2.2240.1791290.1782433X-RAY DIFFRACTION100
2.224-2.2970.2251320.1982353X-RAY DIFFRACTION100
2.297-2.3780.1951360.1532283X-RAY DIFFRACTION100
2.378-2.4670.2011440.1432185X-RAY DIFFRACTION100
2.467-2.5680.1751180.132095X-RAY DIFFRACTION100
2.568-2.6810.161070.1342045X-RAY DIFFRACTION100
2.681-2.8120.1681100.131948X-RAY DIFFRACTION100
2.812-2.9630.1611070.1211853X-RAY DIFFRACTION100
2.963-3.1420.1871010.1331739X-RAY DIFFRACTION100
3.142-3.3580.175850.1511661X-RAY DIFFRACTION100
3.358-3.6260.161760.151558X-RAY DIFFRACTION100
3.626-3.970.153770.1471415X-RAY DIFFRACTION100
3.97-4.4340.113660.1021297X-RAY DIFFRACTION100
4.434-5.1130.141450.1091162X-RAY DIFFRACTION100
5.113-6.2450.137530.122979X-RAY DIFFRACTION100
6.245-8.7580.154360.119768X-RAY DIFFRACTION100
8.758-480.131330.141445X-RAY DIFFRACTION100

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