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- PDB-7aq9: Pseudomonas stutzeri nitrous oxide reductase mutant, H583W -

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Basic information

Entry
Database: PDB / ID: 7aq9
TitlePseudomonas stutzeri nitrous oxide reductase mutant, H583W
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: 1.585 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)145,93325
Polymers144,0132
Non-polymers1,92023
Water19,1141061
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-217 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.385, 76.378, 108.565
Angle α, β, γ (deg.)90.000, 93.370, 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: 72006.617 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, 1084 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 1061 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 38.32 %
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: 1.36998 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: 1.36998 Å / Relative weight: 1
ReflectionResolution: 1.585→69.265 Å / Num. obs: 109368 / % possible obs: 95.1 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 1.59→1.756 Å / Num. unique obs: 5467 / CC1/2: 0.699

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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: 1.585→51.309 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 10674 4.98 %
Rwork0.1562 203494 -
obs0.1583 109374 70.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.95 Å2 / Biso mean: 29.106 Å2 / Biso min: 8.54 Å2
Refinement stepCycle: final / Resolution: 1.585→51.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9094 0 92 1061 10247
Biso mean--38.98 38.36 -
Num. residues----1155
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6621-1.6840.3096430.2993128313
1.684-1.7070.3484820.2875181419
1.707-1.73140.29221180.2819232424
1.7314-1.75730.31251700.2758310933
1.7573-1.78470.27171970.2717409842
1.7847-1.8140.29952680.2706530155
1.814-1.84530.30573720.2551648568
1.8453-1.87880.27124120.2418744178
1.8788-1.9150.2614220.2307815785
1.915-1.95410.25565160.2333899294
1.9541-1.99660.24615390.216946599
1.9966-2.0430.23435930.20099458100
2.043-2.09410.21314760.18379559100
2.0941-2.15070.21075640.1779541100
2.1507-2.2140.20785380.16529449100
2.214-2.28550.21974260.15919632100
2.2855-2.36710.21034920.15869549100
2.3671-2.46190.1964670.15769606100
2.4619-2.5740.19714910.1533953399
2.574-2.70970.20894610.16149508100
2.7097-2.87940.19865030.15819577100
2.8794-3.10170.20695180.1526945699
3.1017-3.41380.18874750.14389552100
3.4138-3.90760.18225390.12249533100
3.9076-4.92260.13834330.09939699100
Refinement TLS params.Method: refined / Origin x: 14.3651 Å / Origin y: 10.2853 Å / Origin z: 26.7379 Å
111213212223313233
T0.1072 Å2-0.019 Å2-0.0197 Å2-0.119 Å2-0.0054 Å2--0.0678 Å2
L0.5927 °20.0918 °2-0.2003 °2-0.7136 °2-0.0265 °2--0.4473 °2
S-0.028 Å °0.1105 Å °0.0061 Å °-0.0909 Å °0.0793 Å °0.008 Å °-0.0842 Å °-0.0536 Å °-0.0259 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 638
2X-RAY DIFFRACTION1allA701 - 1801
3X-RAY DIFFRACTION1allB58 - 643
4X-RAY DIFFRACTION1allB644 - 1206
5X-RAY DIFFRACTION1allD1 - 343

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