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Entry
Database: PDB / ID: 3o5a
TitleCrystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids
Components
  • Diheme cytochrome c napB
  • Periplasmic nitrate reductase
KeywordsOXIDOREDUCTASE / Heterodimeric complex
Function / homology
Function and homology information


nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / anaerobic respiration / cellular respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / anaerobic respiration / cellular respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / membrane / metal ion binding
Similarity search - Function
Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. ...Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Multiheme cytochrome c family profile. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Multiheme cytochrome superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Phosphorylase Kinase; domain 1 / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / HEME C / IRON/SULFUR CLUSTER / : / Periplasmic nitrate reductase / Periplasmic nitrate reductase, electron transfer subunit
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsCoelho, C. / Trincao, J. / Romao, M.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states
Authors: Coelho, C. / Gonzalez, P.J. / Moura, J.J.G. / Moura, I. / Trincao, J. / Romao, M.J.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: 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 / struct_site
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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Jul 22, 2026Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification / _pdbx_entry_details.nonpolymer_details
Revision 2.0Aug 12, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic nitrate reductase
B: Diheme cytochrome c napB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,06526
Polymers105,9532
Non-polymers4,11224
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-27 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.400, 71.410, 128.410
Angle α, β, γ (deg.)90.00, 121.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1160-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Periplasmic nitrate reductase / NapA


Mass: 90560.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalytic subunit / Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: PHG211 / Plasmid: pCM62 / Production host: Cupriavidus necator (bacteria) / Strain (production host): HF210 / References: UniProt: P39185, nitrate reductase
#2: Protein Diheme cytochrome c napB / NapB


Mass: 15392.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: PHG212 / Plasmid: pCM62 / Production host: Cupriavidus necator (bacteria) / Strain (production host): HF210 / References: UniProt: P39186, nitrate reductase (cytochrome)

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Non-polymers , 6 types, 811 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ZW1 / bis-molybdopterin guanine dinucleotide thiol-molybdenum


Mass: 1609.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52MoN20O26P4S5
#7: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE RESIDUE A 900 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. THE HETEROGEN S IS NOW ...THE RESIDUE A 900 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. THE HETEROGEN S IS NOW OBSOLETE IN THE PDB HETGROUP DICTIONARY. IN THIS ENTRY, IT IS TREATED AS A PART OF MOLYBDENUM COMPOUND. OTHER SULFURS OF MOLYBDENUM ATOM ARE SUPPLIED FROM SURROUNDING LIGANDS.

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 15% PEG 3350, 0.2M sodium formate, 0.4M [C4MIM]Cl-, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.72→28.34 Å / Num. all: 130188 / Num. obs: 97895 / % possible obs: 99.6174 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 935 / Redundancy: 3.5 %
Reflection shellResolution: 1.72→1.81 Å / % possible all: 99.6174

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NAP

2nap


Resolution: 1.72→27.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.628 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 4889 5 %RANDOM
Rwork0.14278 ---
all0.1435 154350 --
obs0.14473 93004 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.04 Å2
2--0.07 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.72→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7121 0 248 787 8156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227595
X-RAY DIFFRACTIONr_angle_refined_deg2.312.00710380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7315902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4423.362345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6111554
X-RAY DIFFRACTIONr_chiral_restr0.1980.21067
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215854
X-RAY DIFFRACTIONr_mcbond_it1.2891.54542
X-RAY DIFFRACTIONr_mcangle_it1.93627251
X-RAY DIFFRACTIONr_scbond_it2.97133053
X-RAY DIFFRACTIONr_scangle_it4.3834.53065
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 371 -
Rwork0.176 6716 -
obs--98.51 %

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