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- PDB-7aqa: Pseudomonas stutzeri nitrous oxide reductase mutant, H382A -

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Basic information

Entry
Database: PDB / ID: 7aqa
TitlePseudomonas stutzeri nitrous oxide reductase mutant, H382A
ComponentsNitrous-oxide reductase
KeywordsOXIDOREDUCTASE / periplasmic copper-binding protein
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / 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 / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) ...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 / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / 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 / FORMIC ACID / : / sulfanyl-(tricuprio-$l^{4}-sulfanyl)copper / PHENYLALANINE / (dicuprio-$l^{3}-sulfanyl)-sulfanyl-copper / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsZhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)310656 Germany
German Research Foundation (DFG)192904750 Germany
CitationJournal: Chem Sci / Year: 2021
Title: A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase.
Authors: Zhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O.
History
DepositionOct 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 7, 2021Group: Database references / Non-polymer description / Category: chem_comp / citation / citation_author
Item: _chem_comp.formula / _citation.journal_id_ISSN ..._chem_comp.formula / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,67618
Polymers143,7832
Non-polymers1,89316
Water19,6001088
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13920 Å2
ΔGint-111 kcal/mol
Surface area35510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.824, 76.834, 108.513
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 71891.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19573, nitrous-oxide reductase

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Non-polymers , 11 types, 1104 molecules

#2: Chemical ChemComp-K7E / sulfanyl-(tricuprio-$l^{4}-sulfanyl)copper


Mass: 319.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu4HS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#9: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#10: Chemical ChemComp-RUQ / (dicuprio-$l^{3}-sulfanyl)-sulfanyl-copper


Mass: 255.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu3HS2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.369991 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.369991 Å / Relative weight: 1
ReflectionResolution: 1.497→108.315 Å / Num. obs: 116124 / % possible obs: 86.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.497→1.644 Å / Num. unique obs: 5792 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rkz

6rkz


Resolution: 1.497→62.668 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 11057 4.88 %
Rwork0.1559 215505 -
obs0.1578 115830 63.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.82 Å2 / Biso mean: 29.4773 Å2 / Biso min: 9.47 Å2
Refinement stepCycle: final / Resolution: 1.497→62.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9204 0 75 1088 10367
Biso mean--33.05 39.66 -
Num. residues----1171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5912-1.6130.311990.3084226620
1.613-1.63610.34791490.2899299126
1.6605-1.68650.30052420.2795469041
1.6865-1.71410.30172680.2669532847
1.7141-1.74370.2753080.2616597253
1.7437-1.77540.28953550.2581689861
1.7754-1.80950.26743940.2411749266
1.8095-1.84650.25344220.2313774969
1.8465-1.88660.25365050.2156915082
1.8866-1.93050.24595680.21291027691
1.9305-1.97880.22325660.20331035292
1.9788-2.03230.22135290.18781033892
2.0323-2.09210.21145490.18311039691
2.0921-2.15960.20545650.171031591
2.1596-2.23680.20435030.16151025191
2.2368-2.32640.19895500.16241012190
2.3264-2.43230.2134850.164959585
2.4323-2.56050.18534160.1609983986
2.5605-2.72090.21065500.16151078795
2.7209-2.9310.19325570.15471069995
2.931-3.2260.18515000.14711076695
3.226-3.69270.17935730.12251057893
3.6927-4.65220.14144700.1034969086
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)
10.67910.1609-0.11810.67810.11940.4567-0.0362-0.0157-0.09470.02630.03510.0555-0.007-0.077-0.00310.06310.0007-0.01090.13720.02130.1146.56870.758936.7864
20.6477-0.0751-0.20911.0395-0.09851.08860.06920.1260.0686-0.36440.0892-0.0965-0.247-0.0523-0.04140.2125-0.09310.0390.1128-0.01210.04621.539519.498115.7406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 54:701)A54 - 701
2X-RAY DIFFRACTION2(chain B and resseq 58:701)B58 - 701

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