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- PDB-9evm: High pH (8.0) nitrite-bound MSOX movie series dataset 30 of the c... -

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Basic information

Entry
Database: PDB / ID: 9evm
TitleHigh pH (8.0) nitrite-bound MSOX movie series dataset 30 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [20.7 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
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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, 1items
OrganizationGrant numberCountry
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
DepositionMar 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)40,70410
Polymers39,7581
Non-polymers9469
Water5,423301
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)122,11230
Polymers119,2753
Non-polymers2,83727
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
Unit cell
Length a, b, c (Å)104.56, 104.56, 64.66
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-723-

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(DE3) (bacteria) / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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, 309 molecules

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


Mass: 63.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
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: 0.77491 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: 0.77491 Å / Relative weight: 1
ReflectionResolution: 1.8→45.28 Å / Num. obs: 37438 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.095 / Rrim(I) all: 0.165 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.23 / Num. unique obs: 2237 / CC1/2: 0.365 / Rpim(I) all: 0.873 / Rrim(I) all: 1.518

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
REFMAC5.8.0425phasing
Aimlessdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.002 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.15 / SU B: 2.786 / SU ML: 0.081 / Average fsc free: 0.9708 / Average fsc work: 0.9775 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.099
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1833 1873 5.007 %
Rwork0.1516 35538 -
all0.153 --
obs-37411 99.925 %
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: 28.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.067 Å20.034 Å20 Å2
2--0.067 Å20 Å2
3----0.218 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 51 301 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162745
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.843928
X-RAY DIFFRACTIONr_angle_other_deg0.5531.7596366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4445386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.79858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34710490
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.54610116
X-RAY DIFFRACTIONr_chiral_restr0.0820.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_nbd_refined0.220.2413
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22277
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21279
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.216
X-RAY DIFFRACTIONr_nbd_other0.1480.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_mcbond_it2.112.5361412
X-RAY DIFFRACTIONr_mcbond_other2.1092.5361412
X-RAY DIFFRACTIONr_mcangle_it2.9924.5441780
X-RAY DIFFRACTIONr_mcangle_other2.9924.5461781
X-RAY DIFFRACTIONr_scbond_it3.1782.9721456
X-RAY DIFFRACTIONr_scbond_other3.1782.9731457
X-RAY DIFFRACTIONr_scangle_it4.8045.2612125
X-RAY DIFFRACTIONr_scangle_other4.8025.2612126
X-RAY DIFFRACTIONr_lrange_it6.52631.383064
X-RAY DIFFRACTIONr_lrange_other6.53531.3823064
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
1.8-1.8470.2881440.28826250.28827710.9410.94199.92780.285
1.847-1.8970.2281470.24725210.24626680.960.9551000.243
1.897-1.9520.2621320.2424850.24126170.9540.9581000.23
1.952-2.0120.245980.21324180.21425160.9620.9681000.2
2.012-2.0770.2191280.19623170.19824450.9660.9741000.182
2.077-2.150.221970.17422740.17623720.9670.9899.95780.158
2.15-2.230.2041370.16321650.16623020.9730.9821000.147
2.23-2.3210.2021190.14620800.14921990.9710.9861000.13
2.321-2.4240.1951020.14920060.15121080.9740.9861000.134
2.424-2.5410.2161150.14518980.14920130.9750.9881000.131
2.541-2.6770.156970.14218620.14319590.9840.991000.129
2.677-2.8380.186820.14617210.14818030.9850.9891000.137
2.838-3.0320.209670.14116430.14317130.9760.98899.82490.136
3.032-3.2730.173970.12415180.12716150.9820.991000.124
3.273-3.5810.134640.11714150.11814790.9890.9921000.122
3.581-3.9960.141720.11312730.11513470.9880.99299.85150.125
3.996-4.6010.138640.11211310.11311960.9890.99399.91640.132
4.601-5.6020.14510.1179600.11810130.9870.99299.80260.14
5.602-7.7880.195450.157520.1527980.9790.98699.87470.176
7.788-30.0020.182150.1984740.1984920.9770.97799.39020.234

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