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- PDB-5i5m: Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstitu... -

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Basic information

Entry
Database: PDB / ID: 5i5m
TitleShewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted 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
(R,R)-2,3-BUTANEDIOL / Nitrous-oxide reductase
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)143,16412
Polymers142,3452
Non-polymers81910
Water18,9701053
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-115 kcal/mol
Surface area34580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.756, 56.978, 163.524
Angle α, β, γ (deg.)90.00, 105.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1317-

HOH

21B-1236-

HOH

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Components

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


Mass: 71172.711 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % PEG 3350 0.2 M ammonium sulfate 0.1 M Bis-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: 1.37→47.35 Å / Num. obs: 219234 / % possible obs: 99.3 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i5i

5i5i


Resolution: 1.37→157.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.529 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18067 11354 4.9 %RANDOM
Rwork0.16331 ---
obs0.16417 219234 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0.33 Å2
2---0.38 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.37→157.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9033 0 47 1053 10133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199540
X-RAY DIFFRACTIONr_bond_other_d0.0030.029045
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.94612967
X-RAY DIFFRACTIONr_angle_other_deg1.006320885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75851227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76324.496456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.727151662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7941554
X-RAY DIFFRACTIONr_chiral_restr0.1040.21421
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110907
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022209
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_it0.5160.8284681
X-RAY DIFFRACTIONr_mcbond_other0.5150.8284680
X-RAY DIFFRACTIONr_mcangle_it0.8861.2415869
X-RAY DIFFRACTIONr_mcangle_other0.8861.2425870
X-RAY DIFFRACTIONr_scbond_it0.8110.9384858
X-RAY DIFFRACTIONr_scbond_other0.8050.934851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2881.3527047
X-RAY DIFFRACTIONr_long_range_B_refined3.3678.27643793
X-RAY DIFFRACTIONr_long_range_B_other3.1177.97242704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 794 -
Rwork0.28 15862 -
obs--97.53 %

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