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- PDB-7aq5: Pseudomonas stutzeri nitrous oxide reductase mutant, H583N -

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Basic information

Entry
Database: PDB / ID: 7aq5
TitlePseudomonas stutzeri nitrous oxide reductase mutant, H583N
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 / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION / FORMIC ACID / : / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: J.Am.Chem.Soc. / Year: 2021
Title: Histidine-Gated Proton-Coupled Electron Transfer to the Cu A 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 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,68322
Polymers143,8692
Non-polymers1,81420
Water12,737707
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-229 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.289, 76.452, 109.485
Angle α, β, γ (deg.)90.000, 93.380, 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: 71934.508 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, 727 molecules

#2: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-CUZ / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION


Mass: 286.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu4S / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
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: 1.36998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36998 Å / Relative weight: 1
ReflectionResolution: 1.7→62.647 Å / Num. obs: 98286 / % possible obs: 94.4 % / Redundancy: 6.6 % / CC1/2: 0.993 / Net I/σ(I): 9.9
Reflection shellResolution: 1.705→1.853 Å / Num. unique obs: 4915 / CC1/2: 0.383

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rkz

6rkz


Resolution: 1.7→62.647 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 9503 4.93 %
Rwork0.1614 183090 -
obs0.1632 98297 78.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.58 Å2 / Biso mean: 39.5462 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 1.7→62.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9116 0 89 707 9912
Biso mean--51.34 45.77 -
Num. residues----1159
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7829-1.80640.4375810.3543177023
1.8064-1.83110.44851330.3628233730
1.8573-1.8850.3822870.3311433256
1.885-1.91450.32873270.3019670885
1.9145-1.94590.28713570.2803760998
1.9459-1.97940.27354000.2564788299
1.9794-2.01540.28233670.2401774699
2.0154-2.05420.26234090.2231779499
2.0542-2.09610.23454410.2142769199
2.0961-2.14170.2544400.1989770199
2.1417-2.19150.24183720.1906783999
2.1915-2.24630.23864280.1877761899
2.2463-2.30710.22894420.1811765998
2.3071-2.3750.21593920.171764998
2.375-2.45160.23983700.1686750796
2.4516-2.53920.21094060.1715765398
2.5392-2.64090.20374170.17187852100
2.6409-2.76110.22314610.17457693100
2.7611-2.90670.20784120.17117805100
2.9067-3.08880.20713720.16657818100
3.0888-3.32720.20893490.15727928100
3.3272-3.6620.16814270.14277764100
3.662-4.19190.15873380.1232770798
4.1919-5.28090.15854010.1097760998
Refinement TLS params.Method: refined / Origin x: 14.334 Å / Origin y: 10.2548 Å / Origin z: 26.9091 Å
111213212223313233
T0.1453 Å20.0013 Å2-0.0212 Å2-0.182 Å2-0.0062 Å2--0.1229 Å2
L0.6462 °20.1149 °2-0.2432 °2-1.1627 °2-0.1025 °2--0.6435 °2
S-0.0199 Å °0.1263 Å °0.0312 Å °-0.1387 Å °0.0939 Å °0.0463 Å °-0.091 Å °-0.0759 Å °-0.0524 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA54 - 638
2X-RAY DIFFRACTION1allA701 - 714
3X-RAY DIFFRACTION1allA802 - 1315
4X-RAY DIFFRACTION1allA1401 - 1701
5X-RAY DIFFRACTION1allB58 - 643
6X-RAY DIFFRACTION1allB701 - 710
7X-RAY DIFFRACTION1allB803 - 1203
8X-RAY DIFFRACTION1allC2 - 40

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