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- PDB-6zax: Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. OR... -

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Basic information

Entry
Database: PDB / ID: 6zax
TitleNitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy)
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / substrate-bound / nitrite-bound / low dose / synchrotron
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
sucrose / COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsRose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N013972/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Authors: Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,24417
Polymers38,0871
Non-polymers2,15716
Water8,899494
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

hetero molecules

hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,73151
Polymers114,2613
Non-polymers6,47048
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
crystal symmetry operation5_555z,x,y1
crystal symmetry operation11_456y-1/2,-z+1/2,-x+11
Buried area25310 Å2
ΔGint-380 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.566, 107.566, 107.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-412-

SO4

21A-412-

SO4

31A-737-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 38086.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (strain ORS 375) (bacteria)
Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: Pet26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7, nitrite reductase (NO-forming)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 507 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.72 Å3/Da / Density % sol: 54.83 % / Description: blue cubes
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.6 M (NH4)2SO4 and 50mM HEPES buffer pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.48→48.15 Å / Num. obs: 65671 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Net I/σ(I): 10.8
Reflection shellResolution: 1.48→1.5 Å / Rmerge(I) obs: 1.638 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4753 / CC1/2: 0.541 / Rpim(I) all: 0.667 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THF

6thf


Resolution: 1.48→48.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.315 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3481 5 %RANDOM
Rwork0.1467 ---
obs0.1481 65659 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.41 Å2 / Biso mean: 21.131 Å2 / Biso min: 6.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.48→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 124 532 3322
Biso mean--48.05 35.68 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172799
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6824318
X-RAY DIFFRACTIONr_angle_other_deg1.4581.6016562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0425404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62323.057157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21315499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6541515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023520
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02629
LS refinement shellResolution: 1.48→1.517 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.318 242 -
Rwork0.308 4782 -
obs--99.05 %

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