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- PDB-8s5x: High pH (8.0) as-isolated MSOX movie series dataset 10 of the cop... -

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Basic information

Entry
Database: PDB / ID: 8s5x
TitleHigh pH (8.0) as-isolated MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [3.5 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 / beta-D-fructofuranose / alpha-D-glucopyranose / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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
DepositionFeb 26, 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)40,82211
Polymers39,7581
Non-polymers1,06410
Water9,656536
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)122,46733
Polymers119,2753
Non-polymers3,19130
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 area16420 Å2
ΔGint-282 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.97, 103.97, 64.46
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 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) / Gene: nirK / Plasmid: p22BK / Details (production host): pET-22b(+):blr7089 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking, Oligosaccharide / Class: Nutrient / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking, Oligosaccharide / Class: Nutrient / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 544 molecules

#2: 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
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 536 / 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: 8 / 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: 0.775 Å
DetectorType: DECTRIS PILATUS 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: 1.12→64.46 Å / Num. obs: 151937 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Net I/σ(I): 11.6
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.53 / Num. unique obs: 7527 / CC1/2: 0.455 / Rpim(I) all: 0.862 / Rrim(I) all: 1.774

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→52.468 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.987 / WRfactor Rfree: 0.128 / WRfactor Rwork: 0.106 / SU B: 0.982 / SU ML: 0.019 / Average fsc free: 0.9805 / Average fsc work: 0.9835 / 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
Rfree0.1325 7756 5.106 %
Rwork0.1127 144149 -
all0.114 --
obs-151905 99.994 %
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: 17.355 Å2
Baniso -1Baniso -2Baniso -3
1-0.016 Å20.008 Å2-0 Å2
2--0.016 Å2-0 Å2
3----0.051 Å2
Refinement stepCycle: LAST / Resolution: 1.12→52.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 55 536 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162787
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.8463989
X-RAY DIFFRACTIONr_angle_other_deg0.661.7656461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.23658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48110512
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.29810117
X-RAY DIFFRACTIONr_chiral_restr0.1020.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined0.2420.2459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22513
X-RAY DIFFRACTIONr_nbtor_refined0.180.21322
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2347
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2070.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.217
X-RAY DIFFRACTIONr_nbd_other0.1670.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.268
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_mcbond_it4.7631.3341418
X-RAY DIFFRACTIONr_mcbond_other4.6631.3331418
X-RAY DIFFRACTIONr_mcangle_it6.2412.4011791
X-RAY DIFFRACTIONr_mcangle_other6.332.4041792
X-RAY DIFFRACTIONr_scbond_it6.6731.6411487
X-RAY DIFFRACTIONr_scbond_other6.2521.61464
X-RAY DIFFRACTIONr_scangle_it9.2492.8942168
X-RAY DIFFRACTIONr_scangle_other8.9032.8152133
X-RAY DIFFRACTIONr_lrange_it19.09324.1553314
X-RAY DIFFRACTIONr_lrange_other14.68416.283096
X-RAY DIFFRACTIONr_rigid_bond_restr3.98935692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.12-1.1490.2845930.276106220.276112170.9480.9599.98220.273
1.149-1.1810.2435500.245103420.245108930.9610.95999.99080.24
1.181-1.2150.2335180.208100720.209105900.9630.971000.198
1.215-1.2520.25140.18898080.188103230.9720.97699.99030.175
1.252-1.2930.1815140.17294970.172100110.9790.981000.157
1.293-1.3390.1745490.15291140.15396630.9810.9851000.137
1.339-1.3890.1544540.13789010.13893550.9840.9881000.12
1.389-1.4460.1415020.12584380.12589400.9880.991000.107
1.446-1.510.144240.11182220.11386460.9870.9921000.093
1.51-1.5840.134360.177740.10182100.9890.9941000.081
1.584-1.6690.1244130.0974470.09278600.990.9951000.074
1.669-1.770.1083690.08470890.08574580.9930.9951000.072
1.77-1.8920.1153140.07766790.07969940.9920.99699.98570.071
1.892-2.0440.1023360.07661490.07764860.9940.99699.98460.075
2.044-2.2380.1023030.07756960.07959990.9930.9961000.08
2.238-2.5020.1022590.08151650.08254240.9940.9961000.087
2.502-2.8880.1282350.09745630.09847990.9910.99499.97920.108
2.888-3.5350.1192230.10338470.10440700.9920.9941000.121
3.535-4.9870.1111540.09230240.09331780.9930.9951000.116
4.987-52.4680.109960.15117000.14917970.9940.98499.94440.194

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