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- PDB-2yqb: Structure of P93A variant of three-domain heme-Cu nitrite reducta... -

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Basic information

Entry
Database: PDB / ID: 2yqb
TitleStructure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 A resolution
ComponentsCOPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / PROTON CHANNEL / DENITRIFICATION
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: 1.41 Å
AuthorsAntonyuk, S.V. / Han, C. / Eady, R.R. / Hasnain, S.S.
CitationJournal: Nature / Year: 2013
Title: Structures of protein-protein complexes involved in electron transfer.
Authors: Antonyuk, S.V. / Han, C. / Eady, R.R. / Hasnain, S.S.
History
DepositionNov 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6684
Polymers49,9221
Non-polymers7463
Water14,574809
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)152,00412
Polymers149,7673
Non-polymers2,2379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area17850 Å2
ΔGint-208.9 kcal/mol
Surface area44040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.849, 127.849, 86.628
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-2238-

HOH

21A-2239-

HOH

31A-2261-

HOH

41A-2275-

HOH

51A-2276-

HOH

61A-2472-

HOH

71A-2473-

HOH

81A-2553-

HOH

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Components

#1: Protein COPPER-CONTAINING NITRITE REDUCTASE / NITRITE REDUCTASE


Mass: 49922.477 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA PICKETTII (bacteria) / Strain: 12J / Description: GENBANK ACCESSION NUMBER. NC_010678 / Plasmid: PET26B-RPNIR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E2STD2, UniProt: B2UHR8*PLUS, 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: 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.: 809 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.5
Details: 20MM MES PH 6.5, 20% PEG3350, 0.2M SODIUM CITRATE, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.41→18.08 Å / Num. obs: 102529 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 1.41→1.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AWW

4aww
PDB Unreleased entry


Resolution: 1.41→18.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.626 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14693 5122 5 %RANDOM
Rwork0.11163 ---
obs0.11342 97401 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.41→18.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 45 809 4275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223850
X-RAY DIFFRACTIONr_bond_other_d0.0010.022609
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9975308
X-RAY DIFFRACTIONr_angle_other_deg0.95136442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92324.578166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14315632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7761518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02751
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_it1.5731.52399
X-RAY DIFFRACTIONr_mcbond_other0.5491.5976
X-RAY DIFFRACTIONr_mcangle_it2.2923914
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.56331451
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0694.51354
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.45236459
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.406→1.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 343 -
Rwork0.212 7251 -
obs--99.99 %

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