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- PDB-8r8s: Low pH (5.5) as-isolated MSOX movie series dataset 1 of the coppe... -

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Basic information

Entry
Database: PDB / ID: 8r8s
TitleLow pH (5.5) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.57 MGy]
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / electron transfer
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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsFerroni, F.M. / Antonyuk, S.V. / Rose, S.L. / Eady, R.R. / 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
DepositionNov 29, 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)40,6128
Polymers39,7581
Non-polymers8547
Water9,494527
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

hetero molecules

hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,83624
Polymers119,2753
Non-polymers2,56121
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
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_564-y,x-y+1,z-11
crystal symmetry operation3_454-x+y-1,-x,z-11
Buried area15560 Å2
ΔGint-211 kcal/mol
Surface area35060 Å2
Unit cell
Length a, b, c (Å)103.890, 103.890, 64.490
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-532-

HOH

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Components

#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 diazoefficiens USDA 110 (bacteria)
Strain: USDA110 / Gene: nirK / Plasmid: p22BK / Details (production host): pET-22b(+):blr7089 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: Q89EJ6, nitrite reductase (NO-forming)
#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
#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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8 M ammonium sulfate with 50 mM Hepes buffer (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.85504 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: 0.85504 Å / Relative weight: 1
ReflectionResolution: 1.11→52.42 Å / Num. obs: 154268 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 10.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.035 / Net I/σ(I): 8.9
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.515 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7653 / CC1/2: 0.34 / Rpim(I) all: 0.843 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→52 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.091 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14139 7659 5 %RANDOM
Rwork0.11705 ---
obs0.11827 146576 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.495 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å2-0 Å2
2---0.31 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.11→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 45 527 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132837
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162691
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.6613891
X-RAY DIFFRACTIONr_angle_other_deg1.5221.5896273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.995385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07123.622127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40215487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.561510
X-RAY DIFFRACTIONr_chiral_restr0.1290.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023225
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02604
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_it1.7641.3711391
X-RAY DIFFRACTIONr_mcbond_other1.7141.3681390
X-RAY DIFFRACTIONr_mcangle_it1.7822.0661753
X-RAY DIFFRACTIONr_mcangle_other1.7952.0691754
X-RAY DIFFRACTIONr_scbond_it3.4771.6741446
X-RAY DIFFRACTIONr_scbond_other2.7621.6361430
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8912.3522090
X-RAY DIFFRACTIONr_long_range_B_refined3.6518.643197
X-RAY DIFFRACTIONr_long_range_B_other2.95717.013027
X-RAY DIFFRACTIONr_rigid_bond_restr4.09635528
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.11→1.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 549 -
Rwork0.303 10738 -
obs--98.4 %

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