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- PDB-6zav: NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375... -

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Basic information

Entry
Database: PDB / ID: 6zav
TitleNO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX)
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / NO-bound / product-bound / atomic resolution
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 / NITRIC OXIDE / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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)40,71020
Polymers38,0871
Non-polymers2,62319
Water9,026501
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)122,13060
Polymers114,2613
Non-polymers7,86957
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
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
crystal symmetry operation5_555z,x,y1
crystal symmetry operation11_456y-1/2,-z+1/2,-x+11
Buried area28730 Å2
ΔGint-349 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.467, 107.467, 107.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-509-

EPE

21A-509-

EPE

31A-1059-

HOH

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Components

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Protein / Sugars , 2 types, 5 molecules A

#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: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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, 516 molecules

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


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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.6 Å3/Da / Density % sol: 56 % / Description: blue cubs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6/1.8 M (NH4)2SO3 and 50mM HEPES buffer pH 5/ pH 5.5
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.19→48.06 Å / Num. obs: 166484 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Net I/σ(I): 16.7
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.4 / Num. measured all: 41824 / Num. unique obs: 6441 / CC1/2: 0.508 / Rpim(I) all: 0.572 / Rrim(I) all: 1.476 / Net I/σ(I) obs: 1.4 / % possible all: 97.9

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Processing

Software
NameClassification
SHELXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THF

6thf


Resolution: 1.19→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4%
RfactorNum. reflection% reflectionSelection details
Rfree0.155 6588 5.2 %RANDOM
Rwork0.125 ---
obs0.125 125178 99.9 %-
all-125178 --
Displacement parametersBiso max: 111.53 Å2 / Biso mean: 19.327 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 0 157 502 3322
Biso mean--33.57 38.19 -
Num. residues----345
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.185→1.216 Å
RfactorNum. reflection
Rfree0.272 498
Rwork0.27 -
obs-9194

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