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- PDB-8rgc: High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the c... -

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Basic information

Entry
Database: PDB / ID: 8rgc
TitleHigh pH (8.0) nitrite-bound MSOX movie series dataset 10 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [6.8 MGy]
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper nitrite reductase / Copper-containing nitrite reductase / Br2DNiR / high pH / nitrite-bound / MSOX
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 / CARBON DIOXIDE / COPPER (II) ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. ORS 375 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRose, S.L. / Ferroni, F.M. / Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S.
Funding support United Kingdom, Argentina, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N013972/1 United Kingdom
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2020-00522 Argentina
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
DepositionDec 13, 2023Deposition 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

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,78922
Polymers38,1441
Non-polymers2,64521
Water5,981332
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)122,36766
Polymers114,4323
Non-polymers7,93563
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
Buried area29320 Å2
ΔGint-326 kcal/mol
Surface area34160 Å2
Unit cell
Length a, b, c (Å)107.310, 107.310, 107.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-517-

SO4

21A-517-

SO4

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 38144.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. ORS 375 (bacteria) / Gene: nirK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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 , 7 types, 349 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.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.05 M HEPES pH 5.5, 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: 0.775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.55→47.99 Å / Num. obs: 59803 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 13.3
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2930 / CC1/2: 0.288 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.589 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17072 3128 5.2 %RANDOM
Rwork0.14579 ---
obs0.14709 56627 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 mean: 23.234 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 159 332 3085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162659
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.8633968
X-RAY DIFFRACTIONr_angle_other_deg0.641.7836172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.873513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68310446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it2.0482.2131381
X-RAY DIFFRACTIONr_mcbond_other2.0462.211379
X-RAY DIFFRACTIONr_mcangle_it2.783.9541729
X-RAY DIFFRACTIONr_mcangle_other2.7793.9571730
X-RAY DIFFRACTIONr_scbond_it3.7212.7791519
X-RAY DIFFRACTIONr_scbond_other3.722.7651511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5344.8742214
X-RAY DIFFRACTIONr_long_range_B_refined6.6931.13088
X-RAY DIFFRACTIONr_long_range_B_other6.45826.632988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 232 -
Rwork0.317 4095 -
obs--99.88 %

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