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- PDB-9hs0: Copper-containing nitrite reductase (NirK) from Bradyrhizobium ja... -

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Basic information

Entry
Database: PDB / ID: 9hs0
TitleCopper-containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper-binding protein / Reductase / NirK
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTolmie, C. / Ferroni, F.M. / Opperman, D.J.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Other governmentPICT2020-00522 Argentina
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Structural insights into the copper-containing nitrite reductase from Bradyrhizobium japonicum USDA110 and its role in the low nitrite reductase activity of rhizobia.
Authors: Ramirez, C.S. / Tolmie, C. / Rivas, M.G. / Gonzalez, P.J. / Murgida, D.H. / Opperman, D.J. / Brondino, C.D. / Ferroni, F.M.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8853
Polymers39,7581
Non-polymers1272
Water10,305572
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6569
Polymers119,2753
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_465z-1,x+1,y1
crystal symmetry operation9_456y-1,z,x+11
Buried area13090 Å2
ΔGint-109 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.808, 105.808, 105.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-923-

HOH

21A-980-

HOH

31A-1014-

HOH

41A-1019-

HOH

51A-1030-

HOH

61A-1045-

HOH

71A-1048-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 39758.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Signal peptide: MLPMFTRRAALISAAATALMLATPALA
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Strain: USDA110 / Gene: nirK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.1 M TRIS pH 8.0, 30% w/v PEG 400, 8-15 mg/mL BjNirK

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.19→35.29 Å / Num. obs: 121035 / % possible obs: 95 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.016 / Rrim(I) all: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 1.19→1.25 Å / % possible obs: 70.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.203 / Num. measured all: 26296 / Num. unique obs: 13033 / CC1/2: 0.907 / Rpim(I) all: 0.148 / Rrim(I) all: 0.253 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→35.27 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.699 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.10901 4731 4.9 %RANDOM
Rwork0.09023 ---
obs0.09113 91925 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.268 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 2 572 3133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122817
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162665
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.8253861
X-RAY DIFFRACTIONr_angle_other_deg0.7271.7556178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8825380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.53857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00810474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6771.0011424
X-RAY DIFFRACTIONr_mcbond_other4.68111424
X-RAY DIFFRACTIONr_mcangle_it6.9231.8221803
X-RAY DIFFRACTIONr_mcangle_other6.9291.8241804
X-RAY DIFFRACTIONr_scbond_it5.4591.1731393
X-RAY DIFFRACTIONr_scbond_other5.4631.1741394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3182.0792046
X-RAY DIFFRACTIONr_long_range_B_refined16.99916.9812013
X-RAY DIFFRACTIONr_long_range_B_other11.60513.911188
X-RAY DIFFRACTIONr_rigid_bond_restr4.89635482
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 305 -
Rwork0.133 6731 -
obs--99.82 %

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