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- PDB-9f8x: Low-dose structure of Marinobacter nauticus nitrous oxide reductase -

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Basic information

Entry
Database: PDB / ID: 9f8x
TitleLow-dose structure of Marinobacter nauticus nitrous oxide reductase
ComponentsNitrous-oxide reductase
KeywordsOXIDOREDUCTASE / Nitrogen cycle nitrous oxide N2O reductase denitrification copper-containing enzyme
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane
Similarity search - Function
Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal ...Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DINUCLEAR COPPER ION / [4Cu:2S] cluster / Nitrous-oxide reductase
Similarity search - Component
Biological speciesMarinobacter nauticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsEinsle, O. / Pomowski, A.
Funding support Germany, European Union, Portugal, 10items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276 Germany
German Research Foundation (DFG)311061829 Germany
European Research Council (ERC)310656European Union
Foundation for Science and Technology (FCT)UIDP/04378/2020 Portugal
Foundation for Science and Technology (FCT)UIDB/04378/2020 Portugal
Foundation for Science and Technology (FCT)LA/P/0140/2020 Portugal
Foundation for Science and Technology (FCT)UIDB/50006/2020 Portugal
Foundation for Science and Technology (FCT)UIDP/50006/2020 Portugal
Foundation for Science and Technology (FCT)2022.01152.PTDC Portugal
European Molecular Biology Organization (EMBO)ASTF 282.00-2010European Union
CitationJournal: J.Biol.Inorg.Chem. / Year: 2024
Title: Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus.
Authors: Pomowski, A. / Dell'Acqua, S. / Wust, A. / Pauleta, S.R. / Moura, I. / Einsle, O.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrous-oxide reductase
B: Nitrous-oxide reductase
C: Nitrous-oxide reductase
D: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,96540
Polymers281,8454
Non-polymers3,12036
Water58,0443222
1
A: Nitrous-oxide reductase
B: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,61023
Polymers140,9222
Non-polymers1,68821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-118 kcal/mol
Surface area34860 Å2
MethodPISA
2
C: Nitrous-oxide reductase
D: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,35517
Polymers140,9222
Non-polymers1,43215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13270 Å2
ΔGint-103 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.260, 69.375, 153.188
Angle α, β, γ (deg.)81.384, 77.918, 88.608
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitrous-oxide reductase / N(2)OR / N2O reductase


Mass: 70461.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Marinobacter nauticus (bacteria) / References: UniProt: A0A140IKA4, nitrous-oxide reductase

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Non-polymers , 7 types, 3258 molecules

#2: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu2
#3: Chemical
ChemComp-CUK / [4Cu:2S] cluster


Mass: 318.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 15 % PEG 8000 0.6 M NaCl 0.1 M imidazole/malate protein concentration: 14 mg/ml
Temp details: anoxic glove box

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryostream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 20, 2020 / Details: Varimax HF
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.498→23.501 Å / Num. obs: 381570 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Redundancy: 2 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.026 / Net I/σ(I): 12.1
Reflection shellResolution: 1.498→1.52 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3 / Num. unique obs: 17344 / CC1/2: 0.87 / Rpim(I) all: 0.258 / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DENZOdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.498→23.501 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.833 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1519 19047 4.992 %
Rwork0.1298 362521 -
all0.131 --
obs-381568 91.341 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.832 Å20.006 Å20.534 Å2
2--0.854 Å2-0.079 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.498→23.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18072 0 99 3222 21393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01218979
X-RAY DIFFRACTIONr_bond_other_d0.0020.01616819
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.65825811
X-RAY DIFFRACTIONr_angle_other_deg0.6061.57239301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60652374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.0495113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.613103147
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.10710929
X-RAY DIFFRACTIONr_chiral_restr0.1120.22781
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023778
X-RAY DIFFRACTIONr_nbd_refined0.2020.23498
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.216182
X-RAY DIFFRACTIONr_nbtor_refined0.1750.28829
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.29917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.22344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.259
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.240
X-RAY DIFFRACTIONr_nbd_other0.1750.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2260.277
X-RAY DIFFRACTIONr_mcbond_it1.2331.4769373
X-RAY DIFFRACTIONr_mcbond_other1.2331.4769373
X-RAY DIFFRACTIONr_mcangle_it1.7412.21211788
X-RAY DIFFRACTIONr_mcangle_other1.7422.21311789
X-RAY DIFFRACTIONr_scbond_it2.581.739606
X-RAY DIFFRACTIONr_scbond_other2.581.7319607
X-RAY DIFFRACTIONr_scangle_it3.8542.49113987
X-RAY DIFFRACTIONr_scangle_other3.8542.49113988
X-RAY DIFFRACTIONr_lrange_it5.66127.90522016
X-RAY DIFFRACTIONr_lrange_other5.6627.90522017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.498-1.5370.31112820.288247460.289308620.9690.97684.33670.263
1.537-1.5790.22312860.215247900.216299940.9780.98386.93740.194
1.579-1.6250.19913120.178242890.179292030.980.98687.66560.158
1.625-1.6740.1812350.148238990.15283800.9830.98888.56240.131
1.674-1.7290.16412100.132232510.134274200.9840.9989.20860.118
1.729-1.7890.16111200.126227590.127265560.9840.9989.91940.115
1.789-1.8560.14611600.12220980.122256430.9870.99190.69920.113
1.856-1.9320.1511350.122214850.123247410.9870.99191.42720.118
1.932-2.0170.15411740.127206050.129236370.9860.99192.13940.126
2.017-2.1150.15511170.128198920.13226440.9860.99292.77950.129
2.115-2.2280.1519470.126192310.127215690.9860.99293.55090.13
2.228-2.3620.1439910.115181920.116203710.9880.99394.16820.121
2.362-2.5230.1349810.108172340.11191850.9890.99394.9440.116
2.523-2.7230.1398730.111161750.112178310.9880.99295.60880.121
2.723-2.9780.1457580.118150890.119164510.9870.99196.32850.131
2.978-3.3230.1496750.122137670.124148880.9860.99197.00430.139
3.323-3.8250.1345870.12122240.121131710.9890.99297.26670.139
3.825-4.6540.1275450.112101610.112111830.990.99295.73460.134
4.654-6.4560.1643680.15780690.15786770.990.99197.23410.186
6.456-23.5010.1752910.19345660.19251180.9860.98594.90040.225
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0633-0.0153-0.07780.06170.09580.26150.00120.0078-0.0085-0.0034-0.00140.00680.0294-0.00940.00030.02030.0033-0.00930.012-0.00040.00592.3077-12.3014-9.7276
20.1066-0.0728-0.07560.07340.11390.22270.0203-0.00160.0087-0.0252-0.0041-0.0108-0.0435-0.0048-0.01610.00990.00340.00390.01210.00510.0041-2.15612.10310.0942
30.12180.04910.02660.06560.0730.09120.00320.0131-0.02110.01780.0008-0.01020.0224-0.0017-0.0040.0078-0.0022-0.00220.00390.00260.016230.470414.335658.8445
40.07910.03190.04360.0560.06850.10840-0.01760.01740.0005-0.00360.008-0.0074-0.01160.00360.00640.00070.00170.0065-0.00050.009235.016538.796878.5718
Refinement TLS groupSelection: ALL

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