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- PDB-6gt2: Reduced copper nitrite reductase from Achromobacter cycloclastes ... -

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Basic information

Entry
Database: PDB / ID: 6gt2
TitleReduced copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / FEMTOSECOND / SF-ROX / NITRITE REDUCTASE
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 / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / MALONATE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 1.6 Å
AuthorsHalsted, T.P. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Eady, R.R. / Antonyuk, S.V. / Yamamoto, M. / Hasnain, S.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R000220/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L006960/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Iucrj / Year: 2019
Title: Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography.
Authors: Halsted, T.P. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Blakeley, M.P. / Eady, R.R. / Antonyuk, S.V. / Yamamoto, M. / Hasnain, S.S.
History
DepositionJun 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)41,76311
Polymers40,8191
Non-polymers94310
Water4,630257
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)125,28833
Polymers122,4583
Non-polymers2,83030
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area19390 Å2
ΔGint-33 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.610, 94.610, 94.610
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-726-

HOH

21A-847-

HOH

31A-848-

HOH

41A-850-

HOH

51A-854-

HOH

61A-855-

HOH

71A-856-

HOH

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Components

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


Mass: 40819.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 102.046 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.242 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.242 Å / Relative weight: 1
ReflectionResolution: 1.6→54.62 Å / Num. obs: 37489 / % possible obs: 100 % / Redundancy: 66.1 % / Biso Wilson estimate: 24.9 Å2 / R split: 0.158 / Net I/σ(I): 5.4
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 44.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1858 / R split: 0.708 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / Pulse photon energy: 437.7 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetMotion control: SACLA goniometer
Sample holding: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)
Sample solvent: 3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2.
Support base: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)
Serial crystallography data reductionCrystal hits: 581 / Frames indexed: 410 / Frames total: 581

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
CrystFEL0.6.3data reduction
RefinementResolution: 1.6→54.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.96 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1883 5 %RANDOM
Rwork0.16658 ---
obs0.16823 35562 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.872 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→54.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 58 257 2889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172380
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6813670
X-RAY DIFFRACTIONr_angle_other_deg1.0091.6455567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.4625.348345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25523130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0981512
X-RAY DIFFRACTIONr_chiral_restr0.070.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
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_it1.5932.0071333
X-RAY DIFFRACTIONr_mcbond_other1.582.0031332
X-RAY DIFFRACTIONr_mcangle_it2.2773.0051665
X-RAY DIFFRACTIONr_mcangle_other2.2833.0091666
X-RAY DIFFRACTIONr_scbond_it2.4712.3011376
X-RAY DIFFRACTIONr_scbond_other2.4652.2971374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7263.3372004
X-RAY DIFFRACTIONr_long_range_B_refined4.88924.632906
X-RAY DIFFRACTIONr_long_range_B_other4.72224.1932848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 139 -
Rwork0.257 2578 -
obs--100 %

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