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- PDB-7zcs: Nitrite-bound MSOX movie series dataset 65 (52 MGy) of the copper... -

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Entry
Database: PDB / ID: 7zcs
TitleNitrite-bound MSOX movie series dataset 65 (52 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - water ligand (final)
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Nitrite reductase / Copper nitrite reductase / Copper-containing nitrite reductase / BrNiR / Br2DNiR / 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 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
sucrose / COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. ORS 375 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsRose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Tosha, T. / Kumasaka, T. / Eady, R.R. / Yamamoto, M. / Hasnain, S.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/N013972/1 United Kingdom
UK Research and Innovation (UKRI)BB/S020055/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Authors: Rose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Hedison, T.M. / Shanmugam, M. / Heyes, D.J. / Scrutton, N.S. / Kumasaka, T. / Tosha, T. / Eady, R.R. / Yamamoto, M. / Hasnain, S.S.
History
DepositionMar 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)40,57122
Polymers38,2881
Non-polymers2,28321
Water9,566531
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)121,71366
Polymers114,8653
Non-polymers6,84863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area27170 Å2
ΔGint-399 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.176, 107.176, 107.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21A-987-

HOH

31A-991-

HOH

41A-1005-

HOH

51A-1029-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 38288.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. ORS 375 (bacteria) / Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: PET-26B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7, 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.: 2
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, 550 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.54→75.78 Å / Num. obs: 60762 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.25 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.062 / Net I/σ(I): 5.4
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3027 / CC1/2: 0.328 / Rpim(I) all: 0.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZCR

7zcr


Resolution: 1.61→75.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.625 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19789 2550 5 %RANDOM
Rwork0.16459 ---
obs0.16619 48813 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.528 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.61→75.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 130 531 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133048
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152838
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.6674194
X-RAY DIFFRACTIONr_angle_other_deg1.3451.5946596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6285405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95722.685149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3171516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02671
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_it1.7512.2931441
X-RAY DIFFRACTIONr_mcbond_other1.7522.2911440
X-RAY DIFFRACTIONr_mcangle_it2.5863.431820
X-RAY DIFFRACTIONr_mcangle_other2.5853.4331821
X-RAY DIFFRACTIONr_scbond_it2.8122.781607
X-RAY DIFFRACTIONr_scbond_other2.7452.731570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2923.9642295
X-RAY DIFFRACTIONr_long_range_B_refined7.86931.1623450
X-RAY DIFFRACTIONr_long_range_B_other7.10628.8633235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 147 -
Rwork0.373 2547 -
obs--68.64 %

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