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- PDB-9kwv: Structure of a D98N/C135A/G136A mutant copper-containing nitrite ... -

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Basic information

Entry
Database: PDB / ID: 9kwv
TitleStructure of a D98N/C135A/G136A mutant 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: 0.99 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)36,20311
Polymers35,5041
Non-polymers69910
Water6,684371
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)108,60933
Polymers106,5123
Non-polymers2,09730
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 area13010 Å2
ΔGint-253 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.371, 115.371, 84.336
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

21A-859-

HOH

31A-861-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 35504.039 Da / Num. of mol.: 1 / Mutation: D98N/C135A/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)

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Non-polymers , 5 types, 381 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / 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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 59.57 %
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: 0.99→43 Å / Num. obs: 232705 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Net I/σ(I): 10.5
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.556 / Mean I/σ(I) obs: 1 / Num. unique obs: 11509 / CC1/2: 0.542 / Rpim(I) all: 0.749 / % 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: 0.99→28.84 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 12.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1171 11775 5.06 %
Rwork0.1066 --
obs0.1071 232648 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.99→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 26 371 2726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062848
X-RAY DIFFRACTIONf_angle_d1.0543921
X-RAY DIFFRACTIONf_dihedral_angle_d9.329403
X-RAY DIFFRACTIONf_chiral_restr0.089414
X-RAY DIFFRACTIONf_plane_restr0.008532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-10.30853320.31347413X-RAY DIFFRACTION100
1-1.010.28333550.2887376X-RAY DIFFRACTION100
1.01-1.030.24954090.25647321X-RAY DIFFRACTION100
1.03-1.040.2233980.2437449X-RAY DIFFRACTION100
1.04-1.050.23344190.22327305X-RAY DIFFRACTION100
1.05-1.070.22384580.21437334X-RAY DIFFRACTION100
1.07-1.080.20213810.19527416X-RAY DIFFRACTION100
1.08-1.10.17723840.17317314X-RAY DIFFRACTION100
1.1-1.110.16733860.15657408X-RAY DIFFRACTION100
1.11-1.130.1514230.14087350X-RAY DIFFRACTION100
1.13-1.150.13863730.13297401X-RAY DIFFRACTION100
1.15-1.170.13364380.12697323X-RAY DIFFRACTION100
1.17-1.20.12134160.12387281X-RAY DIFFRACTION100
1.2-1.220.12933650.127411X-RAY DIFFRACTION100
1.22-1.250.13164290.11927376X-RAY DIFFRACTION100
1.25-1.280.11454130.11247298X-RAY DIFFRACTION100
1.28-1.310.12193950.10967304X-RAY DIFFRACTION99
1.31-1.340.11373610.10317393X-RAY DIFFRACTION100
1.34-1.380.09783950.09177378X-RAY DIFFRACTION100
1.38-1.430.0974060.0877343X-RAY DIFFRACTION100
1.43-1.480.09544200.08387369X-RAY DIFFRACTION100
1.48-1.540.09523480.07797406X-RAY DIFFRACTION100
1.54-1.610.09194250.07687311X-RAY DIFFRACTION100
1.61-1.690.08913520.07947344X-RAY DIFFRACTION100
1.69-1.80.09074220.08367344X-RAY DIFFRACTION100
1.8-1.940.09573830.08437394X-RAY DIFFRACTION100
1.94-2.130.09563780.08467389X-RAY DIFFRACTION100
2.13-2.440.09683780.08427322X-RAY DIFFRACTION100
2.44-3.070.10183590.09217416X-RAY DIFFRACTION100
3.08-28.840.11733740.10497384X-RAY DIFFRACTION100

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