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

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Basic information

Entry
Database: PDB / ID: 6zub
TitleCu nitrite reductase from Achromobacter cycloclastes: MSOX series at 170K, dose point 2
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: 1.08 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 22, 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
Water10,178565
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 area15250 Å2
ΔGint-142 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.356, 95.356, 95.356
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-726-

HOH

21A-1052-

HOH

31A-1056-

HOH

41A-1106-

HOH

51A-1118-

HOH

61A-1121-

HOH

71A-1129-

HOH

81A-1139-

HOH

91A-1146-

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, 572 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.: 565 / 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: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6M AMMONIUM SULPHATE, 100MM REMARK 280 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: 1.08→67.427 Å / Num. all: 122039 / Num. obs: 122039 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Rsym value: 0.076 / Net I/av σ(I): 5.3 / Net I/σ(I): 8.5 / Num. measured all: 588965
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.08-1.143.50.61161009173470.3630.7130.611.797.2
1.14-1.2150.4831.185102169350.240.5410.4832.7100
1.21-1.294.90.4730.878446159030.2410.5330.4733.299.9
1.29-1.395.10.326274837147920.1620.3650.3264.3100
1.39-1.5350.212368660136780.1050.2370.2126100
1.53-1.7150.1056.962405123900.0510.1170.1058.999.9
1.71-1.975.10.0842.855231109250.0430.0950.08413.699.8
1.97-2.415.10.0558.94685891980.0270.0620.05520.599.2
2.41-3.425.10.02920.53614270310.0140.0320.02926.697.7
3.42-42.6455.30.02819.22027538400.0130.0310.0283495

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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: 1.08→42.68 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1499 6115 5 %RANDOM
Rwork0.1243 ---
obs0.1256 115825 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.16 Å2 / Biso mean: 12.222 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.08→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 25 588 3187
Biso mean--23.06 29.59 -
Num. residues----333
LS refinement shellResolution: 1.08→1.108 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 433 -
Rwork0.256 8258 -
all-8691 -
obs--95.72 %

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