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- PDB-9kvl: Neutron and X-ray joint refined structure of a copper-containing ... -

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Basic information

Entry
Database: PDB / ID: 9kvl
TitleNeutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) 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 / DEUTERATED WATER / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 5, 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

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5447
Polymers33,0721
Non-polymers4736
Water6,053336
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)100,63321
Polymers99,2153
Non-polymers1,41918
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 area12540 Å2
ΔGint-119 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.060, 115.060, 84.483
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-903-

DOD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 33071.500 Da / Num. of mol.: 1 / Mutation: C135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans 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, 342 molecules

#2: 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
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


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.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: D2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0312.15-4.89
SYNCHROTRONPhoton Factory AR-NW12A20.8
Detector
TypeIDDetectorDate
iBIX1DIFFRACTOMETERJan 28, 2020
DECTRIS PILATUS3 S 2M2PIXELFeb 18, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.151
24.891
30.81
Reflection

Biso Wilson estimate: 6.43 Å2 / Entry-ID: 9KVL

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.7-204344594.67.30.9730.2470.09618.8
1-42.922253161005.10.9960.0760.037213.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.7-1.795.80.565358510.7780.243187.1
1-1.025.10.334.6111710.940.1622100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
STARGazerdata reduction
autoXDSdata reduction
SCALAdata scaling
MOLREPphasing
Refinement

SU ML: 0.11 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.33 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4YSO

4yso

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
1.7-13.2NEUTRON DIFFRACTION0.17180.15560.15642003434424.6194.841
1.3-28.16X-RAY DIFFRACTION0.13160.114410251399.922
Refinement stepCycle: LAST / Resolution: 1.7→13.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 22 336 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025837
X-RAY DIFFRACTIONf_angle_d1.1349808
X-RAY DIFFRACTIONf_dihedral_angle_d16.3351508
X-RAY DIFFRACTIONf_chiral_restr0.088401
X-RAY DIFFRACTIONf_plane_restr0.007927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.14291200.10633400X-RAY DIFFRACTION100
1.32-1.330.11541180.10033405X-RAY DIFFRACTION100
1.33-1.350.11751200.09473426X-RAY DIFFRACTION100
1.35-1.370.13731180.09293435X-RAY DIFFRACTION100
1.37-1.380.11541230.09033426X-RAY DIFFRACTION100
1.38-1.40.12191190.08883418X-RAY DIFFRACTION100
1.4-1.430.12021180.09073390X-RAY DIFFRACTION100
1.43-1.450.10241190.09223388X-RAY DIFFRACTION100
1.45-1.470.10631220.09393472X-RAY DIFFRACTION100
1.47-1.50.11821210.09473387X-RAY DIFFRACTION100
1.5-1.520.10971180.09623418X-RAY DIFFRACTION100
1.52-1.550.12331210.09923434X-RAY DIFFRACTION100
1.55-1.580.11941170.10193417X-RAY DIFFRACTION100
1.59-1.620.13291240.10043430X-RAY DIFFRACTION100
1.62-1.660.11831190.10073372X-RAY DIFFRACTION100
1.66-1.70.11421190.10383435X-RAY DIFFRACTION100
1.7-1.740.12521540.10513399X-RAY DIFFRACTION100
1.74-1.80.11781520.11153357X-RAY DIFFRACTION100
1.8-1.850.13641550.11273412X-RAY DIFFRACTION100
1.85-1.920.12471590.11933340X-RAY DIFFRACTION100
1.92-20.15651640.13363350X-RAY DIFFRACTION100
2-2.090.14841570.12793384X-RAY DIFFRACTION100
2.09-2.20.12711680.12023393X-RAY DIFFRACTION100
2.2-2.340.11661640.11453375X-RAY DIFFRACTION100
2.34-2.520.1391570.11313369X-RAY DIFFRACTION100
2.52-2.770.12671650.11783361X-RAY DIFFRACTION100
2.77-3.170.1461620.12363391X-RAY DIFFRACTION100
3.17-3.990.1441600.13723375X-RAY DIFFRACTION100
3.99-28.160.13971640.13233357X-RAY DIFFRACTION100
1.7-1.740.22671280.19432725NEUTRON DIFFRACTION86
1.74-1.790.21931290.18352733NEUTRON DIFFRACTION88
1.79-1.840.19471320.17472778NEUTRON DIFFRACTION89
1.84-1.90.18331380.17052830NEUTRON DIFFRACTION90
1.9-1.970.17831390.15472824NEUTRON DIFFRACTION91
1.97-2.050.16671380.15182885NEUTRON DIFFRACTION93
2.05-2.140.17131480.1482979NEUTRON DIFFRACTION96
2.14-2.250.15691560.13783141NEUTRON DIFFRACTION99
2.25-2.390.15651480.13343088NEUTRON DIFFRACTION100
2.39-2.580.14231490.13693139NEUTRON DIFFRACTION100
2.58-2.830.17591510.15063101NEUTRON DIFFRACTION100
2.83-3.240.1811490.15963139NEUTRON DIFFRACTION100
3.24-4.060.15831480.15873098NEUTRON DIFFRACTION100
4.06-13.20.14821500.14722979NEUTRON DIFFRACTION95

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