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- PDB-6gtj: Neutron crystal structure for copper nitrite reductase from Achro... -

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Basic information

Entry
Database: PDB / ID: 6gtj
TitleNeutron crystal structure for copper nitrite reductase from Achromobacter Cycloclastes at 1.8 A resolution
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Perdueteration / NITRITE REDUCTASE / electron transfer
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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsAntonyuk, S.V. / Blakeley, M.P. / Halsted, T.P. / Eady, R.R. / 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 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)37,1873
Polymers37,0601
Non-polymers1272
Water3,423190
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)111,5619
Polymers111,1793
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area13930 Å2
ΔGint-40 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.980, 97.980, 97.980
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-681-

HOH

21A-777-

HOH

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Components

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


Mass: 37059.809 Da / Num. of mol.: 1 / Fragment: UNP residues 39-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 35 % / Description: pyramidal shape
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2M Ammonium sulphate, Citrate buffer pH 5 all deuterium based

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: LADI III / Wavelength: 3.05 - 4.00
DetectorType: LADI III / Detector: DIFFRACTOMETER / Date: Jul 24, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
13.051
241
ReflectionResolution: 1.8→40 Å / Num. obs: 24728 / % possible obs: 85.5 % / Redundancy: 6.5 % / Rpim(I) all: 0.063 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1858 / Rpim(I) all: 0.13 / % possible all: 69.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
LaueViewdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BW4

2bw4


Resolution: 1.801→32.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.2764 1145 4.97 %
Rwork0.2317 --
obs0.2339 23020 78.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0045541
NEUTRON DIFFRACTIONf_angle_d0.8849569
NEUTRON DIFFRACTIONf_dihedral_angle_d15.7982069
NEUTRON DIFFRACTIONf_chiral_restr0.063400
NEUTRON DIFFRACTIONf_plane_restr0.005791
LS refinement shellResolution: 1.801→1.8825 Å
RfactorNum. reflection% reflection
Rfree0.3313 98 -
Rwork0.3232 1858 -
obs--54 %

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