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- PDB-7aq2: Pseudomonas stutzeri nitrous oxide reductase mutant, H583A -

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Basic information

Entry
Database: PDB / ID: 7aq2
TitlePseudomonas stutzeri nitrous oxide reductase mutant, H583A
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 / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. ...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, 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: 1.683 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)145,16916
Polymers143,7832
Non-polymers1,38614
Water15,115839
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-236 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.643, 76.501, 108.949
Angle α, β, γ (deg.)90.000, 93.120, 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 , 10 types, 853 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
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: X06DA / Wavelength: 1.36999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36999 Å / Relative weight: 1
ReflectionResolution: 1.683→76.501 Å / Num. obs: 101438 / % possible obs: 92.4 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.683→1.816 Å / Num. unique obs: 5072 / CC1/2: 0.567

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Processing

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

6rkz


Resolution: 1.683→69.54 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 9828 4.95 %
Rwork0.1626 188845 -
obs0.1645 101431 77.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.99 Å2 / Biso mean: 29.9751 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.683→69.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 57 839 9956
Biso mean--28.01 38.3 -
Num. residues----1152
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7429-1.76490.3188870.3126173522
1.7882-1.81270.33111590.2973301438
1.8127-1.83860.3132200.2762388548
1.8386-1.8660.29222770.2706528066
1.866-1.89520.29533110.2656666483
1.8952-1.92620.28154230.2564748393
1.9262-1.95950.27664060.244777996
1.9595-1.99510.26534040.232761495
1.9951-2.03350.26283900.219775396
2.0335-2.0750.23914120.2019775896
2.075-2.12010.22113960.1951776196
2.1201-2.16940.22144260.1843770896
2.1694-2.22370.18354100.1752779797
2.2237-2.28380.2264050.1721779997
2.2838-2.3510.20823600.1683789097
2.351-2.42690.23053960.1668777797
2.4269-2.51360.22963530.1678784097
2.5136-2.61430.2074350.1654783997
2.6143-2.73330.24673940.166791498
2.7333-2.87740.19494130.1656783397
2.8774-3.05770.21533900.163787397
3.0577-3.29370.18023790.1585793798
3.2937-3.62520.20474400.1389787998
3.6252-4.14970.16284750.121788699
4.1497-5.22790.13444630.1065799299
Refinement TLS params.Method: refined / Origin x: 14.8497 Å / Origin y: 10.3985 Å / Origin z: 26.8077 Å
111213212223313233
T0.0947 Å2-0.0078 Å2-0.0192 Å2-0.0985 Å2-0.0018 Å2--0.0672 Å2
L0.4643 °20.0417 °2-0.1716 °2-0.614 °2-0.064 °2--0.3952 °2
S-0.0116 Å °0.0507 Å °0.0149 Å °-0.0941 Å °0.0508 Å °0.0226 Å °-0.0648 Å °-0.0427 Å °0.0038 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA54 - 638
2X-RAY DIFFRACTION1allA701 - 801
3X-RAY DIFFRACTION1allB58 - 644
4X-RAY DIFFRACTION1allD3 - 874
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allE1 - 2
7X-RAY DIFFRACTION1allF2
8X-RAY DIFFRACTION1allG2
9X-RAY DIFFRACTION1allH2
10X-RAY DIFFRACTION1allI1 - 3
11X-RAY DIFFRACTION1allJ2
12X-RAY DIFFRACTION1allK2

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