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- PDB-4n4n: Nitrosomonas europea HAO -

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Basic information

Entry
Database: PDB / ID: 4n4n
TitleNitrosomonas europea HAO
Components
  • Hydroxylamine oxidoreductase
  • hydroxylamine oxidoreductase
KeywordsOXIDOREDUCTASE / C-type cytochrome
Function / homology
Function and homology information


hydroxylamine dehydrogenase / hydroxylamine oxidase activity / hydroxylamine oxidase / anaerobic respiration, using ammonium as electron donor / hydroxylamine oxidoreductase activity / anammoxosome / protein homotrimerization / oxidoreductase activity / heme binding / metal ion binding / identical protein binding
Similarity search - Function
Actin; Chain A, domain 4 - #100 / : / : / Hypothetical protein NE1300 / Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine oxidase / Seven times multi-haem cytochrome CxxCH ...Actin; Chain A, domain 4 - #100 / : / : / Hypothetical protein NE1300 / Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine oxidase / Seven times multi-haem cytochrome CxxCH / : / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Actin; Chain A, domain 4 / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEME C / : / PHOSPHATE ION / Hydroxylamine oxidoreductase / Secreted protein
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaalcke, W.J. / Dietl, A. / Marritt, S.J. / Butt, J.N. / Jetten, M.S.M. / Keltjens, J.T. / Barends, T.R.M.B. / Kartal, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis of Biological NO Generation by Octaheme Oxidoreductases.
Authors: Maalcke, W.J. / Dietl, A. / Marritt, S.J. / Butt, J.N. / Jetten, M.S. / Keltjens, J.T. / Barends, T.R. / Kartal, B.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Apr 9, 2014Group: Experimental preparation
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.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_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.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_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_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 27, 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: Hydroxylamine oxidoreductase
B: hydroxylamine oxidoreductase
C: Hydroxylamine oxidoreductase
D: hydroxylamine oxidoreductase
E: Hydroxylamine oxidoreductase
F: hydroxylamine oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,68632
Polymers203,7086
Non-polymers14,97826
Water19,7081094
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52140 Å2
ΔGint-685 kcal/mol
Surface area57100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.720, 141.970, 106.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hydroxylamine oxidoreductase / HAO


Mass: 61720.473 Da / Num. of mol.: 3 / Fragment: UNP residues 25-528 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q50925, hydroxylamine dehydrogenase
#2: Protein hydroxylamine oxidoreductase


Mass: 6182.173 Da / Num. of mol.: 3 / Fragment: UNP residues 28-84 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q82V11, hydroxylamine dehydrogenase

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Non-polymers , 4 types, 1120 molecules

#3: Chemical...
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 55.82 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: 42% v/v PEG400, 50 mM potassium nitrate, 100 mM MES/NaOH, pH 7.5, MICROBATCH UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
Details: two horizontal deflecting and one vertical deflecting X-ray mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→50.4 Å / Num. all: 98124 / Num. obs: 98124 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.588 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HEIDIdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FGJ

1fgj


Resolution: 2.2→50.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.594 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.266 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21273 10263 9.5 %RANDOM
Rwork0.17928 ---
all0.18246 98124 --
obs0.18246 98124 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.017 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--0.26 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13309 0 1038 1094 15441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0252.14420416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05551674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16424.587654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63152389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9061581
X-RAY DIFFRACTIONr_chiral_restr0.070.21954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.03211568
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2831.58374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.536213489
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72336573
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1244.56927
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.264 751 -
Rwork0.224 7111 -
obs--99.94 %

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