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- PDB-9kwu: D98N/C135A mutant of a copper-containing nitrite reductase in com... -

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Basic information

Entry
Database: PDB / ID: 9kwu
TitleD98N/C135A mutant of a copper-containing nitrite reductase in complex with nitrite
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 / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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)36,0189
Polymers35,4901
Non-polymers5288
Water7,116395
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)108,05427
Polymers106,4703
Non-polymers1,58424
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 area11710 Å2
ΔGint-142 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.334, 115.334, 84.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
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-837-

HOH

21A-855-

HOH

31A-879-

HOH

41A-881-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 35490.012 Da / Num. of mol.: 1 / Mutation: D98N/C135A
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.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M acetate buffer pH 4.5, 5.0% (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: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.12→43 Å / Num. obs: 155451 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 9.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Net I/σ(I): 9.4
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2 / Num. unique obs: 7879 / CC1/2: 0.617 / Rpim(I) all: 0.39 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YSO

4yso


Resolution: 1.12→32.22 Å / SU ML: 0.1149 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 10.5571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1169 7719 4.97 %
Rwork0.1026 147694 -
obs0.1033 155413 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 1.12→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 19 395 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682731
X-RAY DIFFRACTIONf_angle_d1.08313758
X-RAY DIFFRACTIONf_chiral_restr0.0902398
X-RAY DIFFRACTIONf_plane_restr0.0075510
X-RAY DIFFRACTIONf_dihedral_angle_d9.4801385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.3112660.29645084X-RAY DIFFRACTION98.93
1.13-1.150.28353010.26314992X-RAY DIFFRACTION98.79
1.15-1.160.23532340.21985059X-RAY DIFFRACTION98.95
1.16-1.170.20432930.18974999X-RAY DIFFRACTION99.01
1.17-1.190.18312710.16665082X-RAY DIFFRACTION98.95
1.19-1.210.16672570.14855004X-RAY DIFFRACTION98.8
1.21-1.220.14212970.13215012X-RAY DIFFRACTION98.55
1.22-1.240.16382390.12625064X-RAY DIFFRACTION98.51
1.24-1.260.14762700.12224961X-RAY DIFFRACTION98.68
1.26-1.280.12822930.12515067X-RAY DIFFRACTION98.8
1.28-1.30.13632040.13115031X-RAY DIFFRACTION98.59
1.3-1.330.15692420.13625040X-RAY DIFFRACTION98.64
1.33-1.350.14772650.12254980X-RAY DIFFRACTION98.07
1.35-1.380.12392410.09865074X-RAY DIFFRACTION97.95
1.38-1.410.11122220.09424984X-RAY DIFFRACTION97.53
1.41-1.440.10972180.08625004X-RAY DIFFRACTION96.99
1.44-1.480.10612740.08264907X-RAY DIFFRACTION96.28
1.48-1.520.10392180.08044878X-RAY DIFFRACTION95.7
1.52-1.560.0953020.084786X-RAY DIFFRACTION94.85
1.56-1.620.09753070.07974776X-RAY DIFFRACTION94.83
1.62-1.670.09592420.08174828X-RAY DIFFRACTION94.4
1.67-1.740.08022480.07574778X-RAY DIFFRACTION94.16
1.74-1.820.08112010.07694925X-RAY DIFFRACTION94.82
1.82-1.920.09292850.08014737X-RAY DIFFRACTION93.97
1.92-2.030.1022830.08714736X-RAY DIFFRACTION94.11
2.04-2.190.09612750.08934815X-RAY DIFFRACTION94.07
2.19-2.410.10262470.08974796X-RAY DIFFRACTION94.28
2.41-2.760.10912180.09764862X-RAY DIFFRACTION94.6
2.76-3.480.11662630.10174778X-RAY DIFFRACTION93.8
3.48-32.220.12092430.10554655X-RAY DIFFRACTION91.5

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