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- PDB-5i5i: Shewanella denitrificans nitrous oxide reductase, app form -

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Basic information

Entry
Database: PDB / ID: 5i5i
TitleShewanella denitrificans nitrous oxide reductase, app form
ComponentsNitrous-oxide reductase
KeywordsOXIDOREDUCTASE / nitrogen cycle nitrous oxide reductase beta propeller apoprotein
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / 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. / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / YVTN repeat-like/Quinoprotein amine dehydrogenase / Cupredoxin / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nitrous-oxide reductase
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSchneider, L.K. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council310656 Germany
German Research FoundationRTG 1976 Germany
CitationJournal: Biochemistry / Year: 2016
Title: Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase.
Authors: Schneider, L.K. / Einsle, O.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)141,9192
Polymers141,9192
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-49 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.083, 121.624, 178.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 70959.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013) (bacteria)
Gene: nosZ, Sden_2219 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12M27, nitrous-oxide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 3350 0.2 M lithium sulphate 0.1 M Tris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2015
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→101 Å / Num. obs: 67268 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Redundancy: 7.6 % / CC1/2: 0.993 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→100.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.949 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28583 3367 4.9 %RANDOM
Rwork0.23737 ---
obs0.23969 65818 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.326 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--3.28 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.14→100.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8483 0 0 92 8575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198698
X-RAY DIFFRACTIONr_bond_other_d0.0020.028190
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.93811770
X-RAY DIFFRACTIONr_angle_other_deg1.016318853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76951072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3524.289415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.282151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2741549
X-RAY DIFFRACTIONr_chiral_restr0.0980.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.473.2674300
X-RAY DIFFRACTIONr_mcbond_other2.4693.2674299
X-RAY DIFFRACTIONr_mcangle_it3.8944.8895362
X-RAY DIFFRACTIONr_mcangle_other3.8944.895363
X-RAY DIFFRACTIONr_scbond_it3.3253.7544398
X-RAY DIFFRACTIONr_scbond_other3.3253.7554399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4325.4446407
X-RAY DIFFRACTIONr_long_range_B_refined7.73926.3879252
X-RAY DIFFRACTIONr_long_range_B_other7.74126.389241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.139→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 227 -
Rwork0.417 4491 -
obs--92.36 %

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