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- PDB-6gby: Copper nitrite reductase from Achromobacter cycloclastes: non-pol... -

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Basic information

Entry
Database: PDB / ID: 6gby
TitleCopper nitrite reductase from Achromobacter cycloclastes: non-polymorph separated dataset 1
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper / denitrification / serial synchrotron crystallography / polymorphs / 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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / 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 / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsEbrahim, A. / Appleby, M.V. / Axford, D. / Beale, J. / Moreno-Chicano, T. / Sherrell, D.A. / Strange, R.W. / Owen, R.L. / Hough, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022714/1 United Kingdom
Leverhulme TrustRPG-2014-355 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography.
Authors: Ebrahim, A. / Appleby, M.V. / Axford, D. / Beale, J. / Moreno-Chicano, T. / Sherrell, D.A. / Strange, R.W. / Hough, M.A. / Owen, R.L.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.3Jan 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)40,9924
Polymers40,8191
Non-polymers1733
Water2,108117
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)122,97712
Polymers122,4583
Non-polymers5199
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
Unit cell
Length a, b, c (Å)96.870, 96.870, 96.870
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-683-

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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.5
Details: Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5M ammonium sulphate, 0.1M sodium citrate pH 4.5 - in a ratio of 1:3 and ...Details: Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5M ammonium sulphate, 0.1M sodium citrate pH 4.5 - in a ratio of 1:3 and mixed by vortexing for 60s. Microcrystals with a diameter of 5-15 microns grew at room temperature over a periof of 4-6 days

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.48→29.21 Å / Num. obs: 50616 / % possible obs: 100 % / Redundancy: 927 % / CC1/2: 0.997 / R split: 0.0515 / Net I/σ(I): 1.88
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 302 % / Mean I/σ(I) obs: 0.15 / CC1/2: 0.552 / R split: 0.545 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i6k

5i6k


Resolution: 1.48→29.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.892 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27645 2474 4.9 %RANDOM
Rwork0.23506 ---
obs0.2371 48121 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.407 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.48→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 5 117 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192662
X-RAY DIFFRACTIONr_bond_other_d0.0020.022388
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9413635
X-RAY DIFFRACTIONr_angle_other_deg0.96535533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7885341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95624.274117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45115393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7581511
X-RAY DIFFRACTIONr_chiral_restr0.090.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02533
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_it1.3662.3851358
X-RAY DIFFRACTIONr_mcbond_other1.3642.3821357
X-RAY DIFFRACTIONr_mcangle_it2.1653.5691698
X-RAY DIFFRACTIONr_mcangle_other2.1643.5731699
X-RAY DIFFRACTIONr_scbond_it1.7642.5611304
X-RAY DIFFRACTIONr_scbond_other1.7592.5631302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7843.7721935
X-RAY DIFFRACTIONr_long_range_B_refined4.39928.0472775
X-RAY DIFFRACTIONr_long_range_B_other4.39228.052770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 179 -
Rwork0.41 3504 -
obs--100 %

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