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- PDB-6zas: Damage-free as-isolated copper nitrite reductase from Bradyrhizob... -

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Basic information

Entry
Database: PDB / ID: 6zas
TitleDamage-free as-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / as-isolated / damage-free / XFEL
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
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N013972/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Authors: Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)39,27114
Polymers38,0871
Non-polymers1,18413
Water8,737485
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)117,81242
Polymers114,2613
Non-polymers3,55139
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 area20080 Å2
ΔGint-448 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.010, 107.010, 107.010
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-413-

SO4

21A-610-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 38086.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (strain 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.7 Å3/Da / Density % sol: 54.42 % / Description: blue cubes
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 1.6/1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5/ pH 5.5
PH range: 5.0/5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.3→31 Å / Num. obs: 94957 / % possible obs: 100 % / Redundancy: 121 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.981 / R split: 0.115 / Net I/σ(I): 5.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 22.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 12385 / CC1/2: 0.332 / R split: 0.777 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THF

6thf


Resolution: 1.3→30.91 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.777 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20588 5021 5 %RANDOM
Rwork0.15097 ---
obs0.15364 94957 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.045 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 57 485 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172662
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6454092
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5716204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2045386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42922.886149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6481514
X-RAY DIFFRACTIONr_chiral_restr0.090.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
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_it2.972.1971466
X-RAY DIFFRACTIONr_mcbond_other2.9542.1941464
X-RAY DIFFRACTIONr_mcangle_it3.7263.3081842
X-RAY DIFFRACTIONr_mcangle_other3.7293.3111843
X-RAY DIFFRACTIONr_scbond_it3.8732.4521520
X-RAY DIFFRACTIONr_scbond_other3.6262.3681470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0963.4972169
X-RAY DIFFRACTIONr_long_range_B_refined5.48427.1413336
X-RAY DIFFRACTIONr_long_range_B_other4.66225.4913171
X-RAY DIFFRACTIONr_rigid_bond_restr2.73235648
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 362 -
Rwork0.315 6973 -
obs--99.82 %

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