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- PDB-6zu6: Cu nitrite reductase from Achromobacter cycloclastes: MSOX series... -

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Basic information

Entry
Database: PDB / ID: 6zu6
TitleCu nitrite reductase from Achromobacter cycloclastes: MSOX series at 170K, dose point 1
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Cu nitrite reductase / nitrosyl / copper / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / MALONATE ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHough, M.A. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D016290/2 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M020924/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022714/1 United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis.
Authors: Hough, M.A. / Conradie, J. / Strange, R.W. / Antonyuk, S.V. / Eady, R.R. / Ghosh, A. / Hasnain, S.S.
History
DepositionJul 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1358
Polymers36,6211
Non-polymers5137
Water10,431579
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)111,40424
Polymers109,8643
Non-polymers1,54021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area15260 Å2
ΔGint-144 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.340, 95.340, 95.340
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-722-

HOH

21A-1058-

HOH

31A-1064-

HOH

41A-1108-

HOH

51A-1111-

HOH

61A-1123-

HOH

71A-1133-

HOH

81A-1146-

HOH

91A-1148-

HOH

101A-1154-

HOH

111A-1169-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper-containing nitrite reductase / Cu-NIR


Mass: 36621.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 586 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: Crystals were grown using the vapor diffusion hanging drop method with a protein concentration of 10 mg/ml. The reservoir solution consisted of 1.6 M ammonium sulfate and 0.1 M sodium acetate (pH 4.75).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.15→42.6 Å / Num. obs: 101516 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 7 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 9.3
Reflection shellResolution: 1.15→1.21 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14815 / Rpim(I) all: 0.31

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bw4

2bw4


Resolution: 1.15→38.95 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1591 5067 5 %RANDOM
Rwork0.1182 ---
obs0.1202 96370 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.86 Å2 / Biso mean: 12.301 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.15→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 25 612 3211
Biso mean--22.84 30.56 -
Num. residues----333
LS refinement shellResolution: 1.15→1.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 345 -
Rwork0.223 7154 -
all-7499 -
obs--99.89 %

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