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- PDB-7aq0: Pseudomonas stutzeri nitrous oxide reductase mutant, D576A/S550A -

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Basic information

Entry
Database: PDB / ID: 7aq0
TitlePseudomonas stutzeri nitrous oxide reductase mutant, D576A/S550A
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 / : / PHENYLALANINE / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 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)145,86126
Polymers143,5392
Non-polymers2,32224
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-161 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.216, 76.715, 108.996
Angle α, β, γ (deg.)90.000, 93.330, 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: 71769.367 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, 942 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.: 8 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CUZ / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION


Mass: 286.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu4S / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#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.: 2 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 38.89 %
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: 1.37 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 1.584→69.099 Å / Num. obs: 105725 / % possible obs: 95 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 1.586→1.766 Å / Num. unique obs: 5286 / CC1/2: 0.709

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Processing

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

6rkz


Resolution: 1.584→51.343 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 10286 4.97 %
Rwork0.1595 196857 -
obs0.1615 105718 68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.27 Å2 / Biso mean: 27.8167 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.584→51.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9212 0 115 918 10245
Biso mean--37.99 35.63 -
Num. residues----1172
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6016-1.62050.3298150.31262353
1.6402-1.6610.3485360.33238579
1.7059-1.73030.3678960.2882194220
1.7303-1.75610.30791290.2907253326
1.7561-1.78350.31680.2853304932
1.7835-1.81280.29671790.2757382439
1.8128-1.8440.3142510.2614468849
1.844-1.87760.32273150.2567599762
1.8776-1.91370.27664310.2594758279
1.9137-1.95280.26694640.2485884692
1.9528-1.99520.27085350.23489563100
1.9952-2.04160.25386110.22649497100
2.0416-2.09270.25914780.2079694100
2.0927-2.14930.23975300.19449574100
2.1493-2.21250.22675690.17919574100
2.2125-2.28390.22564450.17299703100
2.2839-2.36560.22214990.17339557100
2.3656-2.46030.20644690.1689754100
2.4603-2.57220.20545050.16739639100
2.5722-2.70790.21734550.17179649100
2.7079-2.87750.20985130.16759665100
2.8775-3.09960.20685300.15759568100
3.0996-3.41150.19944850.13729685100
3.4115-3.9050.1585370.11789610100
3.905-4.91930.13124400.09499759100
Refinement TLS params.Method: refined / Origin x: 14.3282 Å / Origin y: 9.8358 Å / Origin z: 26.8341 Å
111213212223313233
T0.1136 Å2-0.0312 Å2-0.024 Å2-0.1385 Å20.0032 Å2--0.087 Å2
L0.5164 °20.0582 °2-0.2138 °2-0.8051 °20.024 °2--0.5627 °2
S-0.0283 Å °0.0589 Å °-0.0024 Å °-0.1385 Å °0.094 Å °0.0093 Å °-0.0927 Å °-0.0691 Å °-0.0343 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 638
2X-RAY DIFFRACTION1allA701 - 1401
3X-RAY DIFFRACTION1allA1501 - 1601
4X-RAY DIFFRACTION1allB58 - 643
5X-RAY DIFFRACTION1allB644 - 1401
6X-RAY DIFFRACTION1allC1 - 109

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