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- PDB-9kwt: Structure of a copper-containing nitrite reductase (D98N/G136A mu... -

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Basic information

Entry
Database: PDB / ID: 9kwt
TitleStructure of a copper-containing nitrite reductase (D98N/G136A mutant) from Geobacillus thermodenitrificans
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper / denitrification
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsFukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom.
Authors: Fukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
History
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)33,71510
Polymers33,1171
Non-polymers5989
Water7,584421
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)101,14530
Polymers99,3503
Non-polymers1,79527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11940 Å2
ΔGint-250 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.126, 115.126, 84.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

21A-908-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 33116.605 Da / Num. of mol.: 1 / Mutation: D98N/G136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Gene: nirK, GTNG_0650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4IL26, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M acetate buffer pH 4.5, 5.5% (w/v) PEG 4000, and 75 mM CuSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→43 Å / Num. obs: 254215 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 8.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Net I/σ(I): 10
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.127 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 12736 / CC1/2: 0.579 / Rpim(I) all: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YSO

4yso


Resolution: 0.96→28.11 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 10.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1067 12841 5.05 %
Rwork0.1004 --
obs0.1007 254173 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.96→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 16 421 2767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062980
X-RAY DIFFRACTIONf_angle_d1.1654105
X-RAY DIFFRACTIONf_dihedral_angle_d7.879421
X-RAY DIFFRACTIONf_chiral_restr0.089433
X-RAY DIFFRACTIONf_plane_restr0.008559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.970.26564250.27538121X-RAY DIFFRACTION100
0.97-0.980.2694130.24358044X-RAY DIFFRACTION100
0.98-0.990.23184320.2268037X-RAY DIFFRACTION100
0.99-1.010.23164400.20958113X-RAY DIFFRACTION100
1.01-1.020.20474180.19258083X-RAY DIFFRACTION100
1.02-1.030.1824370.17838056X-RAY DIFFRACTION100
1.03-1.050.16174290.16448077X-RAY DIFFRACTION100
1.05-1.060.15154360.15958057X-RAY DIFFRACTION100
1.06-1.080.15854150.1488074X-RAY DIFFRACTION100
1.08-1.10.13984390.12988081X-RAY DIFFRACTION100
1.1-1.120.1234450.11788027X-RAY DIFFRACTION100
1.12-1.140.10614370.10928023X-RAY DIFFRACTION100
1.14-1.160.10683830.10128145X-RAY DIFFRACTION100
1.16-1.180.10714680.09818008X-RAY DIFFRACTION100
1.18-1.210.10184750.09778062X-RAY DIFFRACTION100
1.21-1.240.1154650.09617981X-RAY DIFFRACTION100
1.24-1.270.09823820.09328108X-RAY DIFFRACTION100
1.27-1.30.10144520.09198029X-RAY DIFFRACTION100
1.3-1.340.09154380.08828070X-RAY DIFFRACTION100
1.34-1.380.09144150.08078065X-RAY DIFFRACTION100
1.38-1.430.08243910.07878078X-RAY DIFFRACTION100
1.43-1.490.09543950.0778064X-RAY DIFFRACTION100
1.49-1.560.08194160.07638064X-RAY DIFFRACTION100
1.56-1.640.09064490.07588029X-RAY DIFFRACTION100
1.64-1.740.09364260.07687996X-RAY DIFFRACTION99
1.74-1.880.08394260.08238007X-RAY DIFFRACTION99
1.88-2.070.08844240.08687998X-RAY DIFFRACTION99
2.07-2.370.09374480.08637899X-RAY DIFFRACTION98
2.37-2.980.09344060.09247993X-RAY DIFFRACTION99
2.98-28.110.10964160.10497943X-RAY DIFFRACTION98

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