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- PDB-6fja: Crystal structure of T2D three-domain heme-Cu nitrite reductase f... -

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Basic information

Entry
Database: PDB / ID: 6fja
TitleCrystal structure of T2D three-domain heme-Cu nitrite reductase from Ralstonia pickettii
ComponentsNitrite reductase
KeywordsELECTRON TRANSPORT / nitrite reductase / electron transfer / redox reactions / tyrosine activation
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. ...: / Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAntonyuk, S.V. / Eady, R. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006960/1 United Kingdom
CitationJournal: To be published
Title: Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases
Authors: Dong, J. / Sasaki, D. / Eady, R. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJan 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6313
Polymers49,9491
Non-polymers6822
Water7,873437
1
A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8929
Polymers149,8463
Non-polymers2,0466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17520 Å2
ΔGint-168 kcal/mol
Surface area43960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.230, 128.230, 86.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-951-

HOH

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Components

#1: Protein Nitrite reductase


Mass: 49948.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I6NAW4, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.75 Å3/Da / Density % sol: 55 % / Description: droplet like
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: Bis-Tris propane, 01M citrate, 22% P3350 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→46.66 Å / Num. obs: 26499 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.067 / Net I/av σ(I): 9.2 / Net I/σ(I): 0.993
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1798 / CC1/2: 0.559 / Rpim(I) all: 0.43 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZIY

3ziy


Resolution: 2.2→46.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.123 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17538 1343 5.1 %RANDOM
Rwork0.13608 ---
obs0.13807 25151 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---1.22 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 44 437 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193563
X-RAY DIFFRACTIONr_bond_other_d0.0020.023355
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9734856
X-RAY DIFFRACTIONr_angle_other_deg0.93337729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36824.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09315542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214104
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02807
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_it1.4572.8031819
X-RAY DIFFRACTIONr_mcbond_other1.4572.81818
X-RAY DIFFRACTIONr_mcangle_it2.1954.1982272
X-RAY DIFFRACTIONr_mcangle_other2.1954.2012273
X-RAY DIFFRACTIONr_scbond_it2.6353.1141742
X-RAY DIFFRACTIONr_scbond_other2.6363.1141740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3384.5432582
X-RAY DIFFRACTIONr_long_range_B_refined7.62824.4194306
X-RAY DIFFRACTIONr_long_range_B_other7.27523.614117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 86 -
Rwork0.244 1704 -
obs--90.96 %

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