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- PDB-8ru9: High pH (8.0) nitrite-bound MSOX movie series dataset 1 of the co... -

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Basic information

Entry
Database: PDB / ID: 8ru9
TitleHigh pH (8.0) nitrite-bound MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.69 MGy]
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / electron transfer / Nitrite binding / nitrite reductase
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, 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: 1.1 Å
AuthorsRose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, A.L. / Antonyuk, S.V. / Hasnain, S.S.
Funding support Argentina, United Kingdom, 2items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2020-00522 Argentina
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N013972/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases.
Authors: Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.name / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,75410
Polymers39,7581
Non-polymers9969
Water9,548530
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,26230
Polymers119,2753
Non-polymers2,98727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area17820 Å2
ΔGint-248 kcal/mol
Surface area33850 Å2
Unit cell
Length a, b, c (Å)103.92, 103.92, 64.25
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-762-

HOH

21A-950-

HOH

31A-954-

HOH

41A-968-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 39758.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: ORS375 / Gene: nirK / Plasmid: p22BK / Details (production host): pET-22b(+):blr7089 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q89EJ6, 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.: 1 / Source method: obtained synthetically
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 , 4 types, 538 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.77492 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77492 Å / Relative weight: 1
ReflectionResolution: 1.1→45.039 Å / Num. obs: 159037 / % possible obs: 99.6 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.05 / Rrim(I) all: 0.085 / Net I/σ(I): 8.1
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.115 / Num. unique obs: 11033 / CC1/2: 0.313 / Rpim(I) all: 0.858 / Rrim(I) all: 1 / % possible all: 99.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→45.039 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.985 / WRfactor Rfree: 0.131 / WRfactor Rwork: 0.112 / SU B: 0.988 / SU ML: 0.019 / Average fsc free: 0.9757 / Average fsc work: 0.9781 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.023
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1374 8211 5.164 %
Rwork0.1197 150796 -
all0.121 --
obs-159007 99.616 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.108 Å2-0.054 Å20 Å2
2---0.108 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 53 530 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122888
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162755
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.8383963
X-RAY DIFFRACTIONr_angle_other_deg0.6481.7546389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.02458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64110488
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.12810117
X-RAY DIFFRACTIONr_chiral_restr0.10.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_nbd_refined0.2750.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22456
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21304
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2361
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4140.22
X-RAY DIFFRACTIONr_metal_ion_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.222
X-RAY DIFFRACTIONr_nbd_other0.1550.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.287
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_mcbond_it4.7051.2651422
X-RAY DIFFRACTIONr_mcbond_other4.691.2641422
X-RAY DIFFRACTIONr_mcangle_it6.6642.2761793
X-RAY DIFFRACTIONr_mcangle_other6.672.2781794
X-RAY DIFFRACTIONr_scbond_it5.9281.4791466
X-RAY DIFFRACTIONr_scbond_other5.461.4511447
X-RAY DIFFRACTIONr_scangle_it8.0072.6272146
X-RAY DIFFRACTIONr_scangle_other7.5942.5722117
X-RAY DIFFRACTIONr_lrange_it15.79221.9863324
X-RAY DIFFRACTIONr_lrange_other1215.763100
X-RAY DIFFRACTIONr_rigid_bond_restr3.97935643
LS refinement shellResolution: 1.1→1.129 Å
RfactorNum. reflection% reflection
Rfree0.3 636 -
Rwork0.289 11033 -
obs--99.2684 %

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