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- PDB-9kws: D98N mutant of a copper-containing nitrite reductase from Geobaci... -

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Basic information

Entry
Database: PDB / ID: 9kws
TitleD98N mutant of a copper-containing nitrite reductase 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
ACETIC ACID / COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsFukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,09911
Polymers35,5221
Non-polymers57710
Water7,692427
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)108,29833
Polymers106,5663
Non-polymers1,73230
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 area12370 Å2
ΔGint-269 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.038, 115.038, 84.403
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-852-

HOH

21A-912-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 35522.078 Da / Num. of mol.: 1 / Mutation: D98N
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 , 6 types, 437 molecules

#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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
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: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→42.9 Å / Num. obs: 193408 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.037 / Net I/σ(I): 11.1
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9589 / CC1/2: 0.803 / Rpim(I) all: 0.277 / % possible all: 100

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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: 1.05→26.26 Å / SU ML: 0.0947 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 7.4529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1007 9571 4.95 %
Rwork0.0896 183805 -
obs0.0901 193376 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.56 Å2
Refinement stepCycle: LAST / Resolution: 1.05→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 20 427 2761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062874
X-RAY DIFFRACTIONf_angle_d1.08643969
X-RAY DIFFRACTIONf_chiral_restr0.0872416
X-RAY DIFFRACTIONf_plane_restr0.008544
X-RAY DIFFRACTIONf_dihedral_angle_d7.7643412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.2663350.25736183X-RAY DIFFRACTION100
1.06-1.070.22463510.21836134X-RAY DIFFRACTION99.94
1.07-1.090.1953270.18316146X-RAY DIFFRACTION99.94
1.09-1.10.15363200.15736070X-RAY DIFFRACTION99.95
1.1-1.120.14363050.1276219X-RAY DIFFRACTION99.88
1.12-1.130.1223520.11096128X-RAY DIFFRACTION99.88
1.13-1.150.09763240.10096153X-RAY DIFFRACTION99.91
1.15-1.160.10722860.09496179X-RAY DIFFRACTION99.91
1.16-1.180.10563710.09596158X-RAY DIFFRACTION99.89
1.18-1.20.10692870.09886169X-RAY DIFFRACTION99.86
1.2-1.220.1133240.10236170X-RAY DIFFRACTION99.82
1.22-1.240.11933420.10596137X-RAY DIFFRACTION99.82
1.24-1.270.11672930.10216147X-RAY DIFFRACTION99.98
1.27-1.290.08453230.08436121X-RAY DIFFRACTION99.95
1.29-1.320.09863110.08156165X-RAY DIFFRACTION99.89
1.32-1.350.09353440.07626142X-RAY DIFFRACTION99.92
1.35-1.390.09483410.07436168X-RAY DIFFRACTION99.95
1.39-1.430.08063240.07126110X-RAY DIFFRACTION99.84
1.43-1.470.07993220.07036154X-RAY DIFFRACTION99.88
1.47-1.510.07372420.06996212X-RAY DIFFRACTION99.6
1.51-1.570.08672960.07156163X-RAY DIFFRACTION99.26
1.57-1.630.08133320.07136058X-RAY DIFFRACTION99.02
1.63-1.710.08632980.0726124X-RAY DIFFRACTION99.23
1.71-1.80.07523100.07316137X-RAY DIFFRACTION99.2
1.8-1.910.08492950.07986080X-RAY DIFFRACTION98.79
1.91-2.050.10033410.08436072X-RAY DIFFRACTION98.36
2.06-2.260.09423200.08326019X-RAY DIFFRACTION97.72
2.26-2.590.09383050.08736017X-RAY DIFFRACTION97.64
2.59-3.260.10523210.096042X-RAY DIFFRACTION98.21
3.26-26.260.10623290.09526028X-RAY DIFFRACTION97.94

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