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- PDB-6zat: Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. OR... -

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Basic information

Entry
Database: PDB / ID: 6zat
TitleNitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.0 A resolution (unrestrained full matrix refinement by SHELX)
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing / BrNiR / Br2dNiR / nitrite-bound / substrate-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
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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)40,07421
Polymers38,0871
Non-polymers1,98720
Water12,611700
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)120,22163
Polymers114,2613
Non-polymers5,96060
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 area26490 Å2
ΔGint-478 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.786, 106.786, 106.786
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-516-

SO4

21A-516-

SO4

31A-520-

EPE

41A-1085-

HOH

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Components

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Protein , 1 types, 1 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 (bacteria) / Strain (production host): DE3 / References: UniProt: H0SLX7, nitrite reductase (NO-forming)

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Non-polymers , 6 types, 720 molecules

#2: 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
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / 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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 54.13 % / Description: blue big cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6/1.8 M (NH4)2SO4 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: Diamond / Beamline: I03 / Wavelength: 0.86999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2019 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86999 Å / Relative weight: 1
ReflectionResolution: 1→53.39 Å / Num. obs: 216881 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 6.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Net I/av σ(I): 10.8 / Net I/σ(I): 10.8
Reflection shellResolution: 1→1.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10633 / CC1/2: 0.388 / Rpim(I) all: 0.731 / % possible all: 94.6

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Processing

Software
NameVersionClassification
SHELXL-97refinement
DIALSdata reduction
xia2data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THF

6thf


Resolution: 1→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.015 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4%
RfactorNum. reflection% reflectionSelection details
Rfree0.1429 8133 5.3 %RANDOM
Rwork0.126 ---
obs-205980 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16 Å2
Refine analyzeNum. disordered residues: 139 / Occupancy sum hydrogen: 2485 / Occupancy sum non hydrogen: 3350.3
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 114 771 3661
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
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→1.026 Å
RfactorNum. reflection% reflection
Rfree0.28 855 -
Rwork0.276 14990 -
obs--99.29 %

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