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- PDB-6tfd: Crystal structure of nitrite and NO bound three-domain copper-con... -

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Basic information

Entry
Database: PDB / ID: 6tfd
TitleCrystal structure of nitrite and NO bound three-domain copper-containing nitrite reductase from Hyphomicrobium denitrificans strain 1NES1
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper-containing nitrite reductase / Hyphomicrobium denitrificans strain 1NES1 / electron transfer
Function / homology
Function and homology information


nitrite reductase (NO-forming) / : / nitrite reductase (NO-forming) activity / electron transfer activity / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesHyphomicrobium denitrificans 1NES1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSasaki, D. / Watanabe, T.F. / Eady, R.R. / Garratt, R.C. / Antonyuk, S.V. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Iucrj / Year: 2020
Title: Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes.
Authors: Sasaki, D. / Watanabe, T.F. / Eady, R.R. / Garratt, R.C. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionNov 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / software / 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_asym_id / _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_asym_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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,84715
Polymers147,1533
Non-polymers69412
Water11,512639
1
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,69330
Polymers294,3066
Non-polymers1,38824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area33270 Å2
ΔGint-256 kcal/mol
Surface area80240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.722, 77.722, 758.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49050.926 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium denitrificans 1NES1 (bacteria)
Gene: HYPDE_25578 / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: N0B9M5, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.35 % / Description: Hexagonal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 22.5% (v/v) PEG Smear Low, 0.1 M Sodium cacodylate pH5.3 0.2 M Ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→126.37 Å / Num. obs: 81889 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 45.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.064 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.845 / Mean I/σ(I) obs: 0.855 / Num. unique obs: 3922 / CC1/2: 0.4256 / Rpim(I) all: 0.828 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata processing
Aimless0.7.4data scaling
MOLREP11.6.04phasing
Coot0.8.9.1model building
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DV6

2dv6


Resolution: 2.25→126.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.093 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 3336 5 %RANDOM
Rwork0.172 ---
obs0.1747 63709 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.29 Å2 / Biso mean: 50.816 Å2 / Biso min: 30.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.73 Å20 Å2
2--1.45 Å20 Å2
3----4.71 Å2
Refinement stepCycle: final / Resolution: 2.25→126.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9605 0 17 639 10261
Biso mean--52.34 52.6 -
Num. residues----1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179000
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.64513446
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5720879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.70551270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49422.417480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.318151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.751552
X-RAY DIFFRACTIONr_chiral_restr0.0690.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022046
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 246 -
Rwork0.337 4576 -
obs--99.98 %

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