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- PDB-8rfp: Low pH (5.5) nitrite-bound MSOX movie series dataset 3 of the cop... -

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Basic information

Entry
Database: PDB / ID: 8rfp
TitleLow pH (5.5) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [3.06 MGy] - nitrite/NO intermediate
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper nitrite reductase / Copper-containing nitrite reductase / BrJNiR / low 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 / COPPER (II) ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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. / Martin Ferroni, F. / Horrell, S. / Dante Brondino, C. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Samar Hasnain, S.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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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)38,32014
Polymers37,1061
Non-polymers1,21413
Water7,152397
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)114,96042
Polymers111,3193
Non-polymers3,64139
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 area19150 Å2
ΔGint-293 kcal/mol
Surface area34350 Å2
Unit cell
Length a, b, c (Å)104.210, 104.210, 64.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-831-

HOH

31A-859-

HOH

41A-864-

HOH

51A-878-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 37106.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: nirK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89EJ6
#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: 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, 409 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.: 3 / 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.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 397 / 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: 54.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M 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: 0.855 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.855 Å / Relative weight: 1
ReflectionResolution: 1.23→45.12 Å / Num. obs: 114182 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 10.7
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5592 / CC1/2: 0.333 / Rpim(I) all: 0.84 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→30 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.441 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13767 5838 5.1 %RANDOM
Rwork0.11431 ---
obs0.11549 108320 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å2-0 Å2
2---0.22 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.23→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 66 397 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122864
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162694
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.8463914
X-RAY DIFFRACTIONr_angle_other_deg0.6651.776273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8155385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.33359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72410484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023325
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02609
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_it4.7051.7011400
X-RAY DIFFRACTIONr_mcbond_other4.6651.71399
X-RAY DIFFRACTIONr_mcangle_it6.4723.0611765
X-RAY DIFFRACTIONr_mcangle_other6.4763.0631766
X-RAY DIFFRACTIONr_scbond_it6.7972.0251464
X-RAY DIFFRACTIONr_scbond_other6.4221.9851434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1013.5162089
X-RAY DIFFRACTIONr_long_range_B_refined13.57527.983147
X-RAY DIFFRACTIONr_long_range_B_other11.97921.643006
X-RAY DIFFRACTIONr_rigid_bond_restr3.84235558
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 435 -
Rwork0.301 7972 -
obs--98.37 %

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