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- PDB-8s2q: High pH (8.0) as-isolated MSOX movie series dataset 2 of the copp... -

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Basic information

Entry
Database: PDB / ID: 8s2q
TitleHigh pH (8.0) as-isolated MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.7 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: 1.05 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 18, 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
Water9,530529
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 area16440 Å2
ΔGint-285 kcal/mol
Surface area35150 Å2
Unit cell
Length a, b, c (Å)103.82, 103.82, 64.35
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) / 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)

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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, 537 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.: 529 / 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-F / 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: 1.05→64.35 Å / Num. obs: 183378 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.042 / Rrim(I) all: 0.093 / Net I/σ(I): 11.8
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.732 / Num. unique obs: 8110 / CC1/2: 0.386 / Rpim(I) all: 0.995 / Rrim(I) all: 2.022

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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: 1.05→52.383 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.747 / SU ML: 0.015 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.019
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1295 9116 4.972 %
Rwork0.1147 174228 -
all0.115 --
obs-183344 99.995 %
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: 16.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.018 Å20.009 Å2-0 Å2
2--0.018 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.05→52.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 55 529 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162804
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.8463989
X-RAY DIFFRACTIONr_angle_other_deg0.6931.7656508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8615398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.0758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6510512
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2410117
X-RAY DIFFRACTIONr_chiral_restr0.1050.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
X-RAY DIFFRACTIONr_nbd_refined0.2510.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22525
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21324
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2386
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.218
X-RAY DIFFRACTIONr_nbd_other0.1830.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.263
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_mcbond_it5.7461.2741418
X-RAY DIFFRACTIONr_mcbond_other5.4641.2721418
X-RAY DIFFRACTIONr_mcangle_it7.7662.291791
X-RAY DIFFRACTIONr_mcangle_other7.8792.2951792
X-RAY DIFFRACTIONr_scbond_it6.3211.5351487
X-RAY DIFFRACTIONr_scbond_other5.9361.4991464
X-RAY DIFFRACTIONr_scangle_it8.9562.7162168
X-RAY DIFFRACTIONr_scangle_other8.6582.6472133
X-RAY DIFFRACTIONr_lrange_it19.32521.8223368
X-RAY DIFFRACTIONr_lrange_other14.52915.6613128
X-RAY DIFFRACTIONr_rigid_bond_restr4.06935709
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
1.05-1.0770.3076400.299128610.299135050.9380.9499.97040.299
1.077-1.1070.2827160.266124490.267131650.950.9561000.265
1.107-1.1390.2316340.223121840.224128180.9660.9691000.218
1.139-1.1740.2076400.19118360.191124780.9730.97799.9840.18
1.174-1.2120.1635880.16114350.16120230.9820.9831000.147
1.212-1.2550.1575900.145110940.145116840.9840.9861000.13
1.255-1.3020.1485120.133107860.134112990.9860.98999.99110.118
1.302-1.3550.1385650.12102740.121108390.9880.9911000.105
1.355-1.4160.1315250.10998550.11103800.9890.9931000.095
1.416-1.4850.1145040.09794760.09899800.9920.9941000.084
1.485-1.5650.0994530.08589990.08594520.9940.9961000.074
1.565-1.660.0984570.07884940.07989510.9940.9961000.07
1.66-1.7740.0984070.07780390.07884460.9940.9961000.072
1.774-1.9160.0923760.07674680.07778440.9950.9971000.074
1.916-2.0990.0983420.08268860.08372280.9940.9961000.084
2.099-2.3460.0933270.08362290.08465560.9950.9961000.09
2.346-2.7080.1142830.09555220.09658060.9920.99499.98280.106
2.708-3.3140.1312670.11246390.11349060.990.9931000.132
3.314-4.6780.1091930.10136300.10138230.9940.9941000.127
4.678-52.3830.165970.15420720.15421700.9790.98699.95390.205

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