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- PDB-6tfo: Crystal structure of as isolated three-domain copper-containing n... -

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Basic information

Entry
Database: PDB / ID: 6tfo
TitleCrystal structure of as isolated 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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesHyphomicrobium denitrificans 1NES1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 14, 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 / 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 / _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

Downloads & links

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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)147,72512
Polymers147,1533
Non-polymers5729
Water9,512528
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)295,44924
Polymers294,3066
Non-polymers1,14418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area32040 Å2
ΔGint-267 kcal/mol
Surface area79410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.072, 77.072, 754.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-695-

HOH

21C-766-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A39 - 459
2010B39 - 459
1020A38 - 459
2020C38 - 459
1030B39 - 459
2030C39 - 459

NCS ensembles :
ID
1
2
3

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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


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.16 % / Description: Hexagonal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% (w/v) PEG 1,000, 0.1 M Sodium citrate tribasic dihydrate pH5.5, 0.1 M Lithium sulfate monohydrate

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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: 2.05→66.75 Å / Num. obs: 85026 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.084 / Net I/σ(I): 3.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.926 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4402 / CC1/2: 0.61 / Rpim(I) all: 0.677 / % possible all: 98.2

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Processing

Software
NameVersionClassification
DIALS1.14.25data processing
Aimless0.7.4data scaling
MOLREP11.6.04phasing
Coot0.8.9.1model building
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DV6

2dv6


Resolution: 2.05→66.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.722 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.208
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 4195 5 %RANDOM
Rwork0.2271 ---
obs0.2297 80428 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.68 Å2 / Biso mean: 47.868 Å2 / Biso min: 30.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å21.05 Å20 Å2
2--2.1 Å20 Å2
3----6.82 Å2
Refinement stepCycle: final / Resolution: 2.05→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9612 0 9 528 10149
Biso mean--46.68 50.48 -
Num. residues----1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179005
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.64513450
X-RAY DIFFRACTIONr_angle_other_deg1.2481.5720896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6351270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37322.5480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.595151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0511551
X-RAY DIFFRACTIONr_chiral_restr0.0650.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022041
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A132190.08
12B132190.08
21A133320.07
22C133320.07
31B132410.07
32C132410.07
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.442 312 -
Rwork0.43 5797 -
obs--98.52 %

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