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- PDB-4n4o: Nitrosomonas europea HAO soaked in NH2OH -

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Basic information

Entry
Database: PDB / ID: 4n4o
TitleNitrosomonas europea HAO soaked in NH2OH
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 / identical protein binding / metal ion 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 / HYDROXYAMINE / : / PHOSPHATE ION / Hydroxylamine oxidoreductase / Secreted protein
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.472 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 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

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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)219,87837
Polymers203,7086
Non-polymers16,17131
Water17,889993
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53870 Å2
ΔGint-671 kcal/mol
Surface area56680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.090, 141.960, 106.480
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 , 6 types, 1024 molecules

#3: Chemical...
ChemComp-HEC / HEME C / 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-HOA / HYDROXYAMINE / Hydroxylamine


Mass: 33.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H3NO
#6: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 993 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
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: SLS / Beamline: X10SA / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.472→50 Å / Num. all: 68039 / Num. obs: 68039 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 11
Reflection shellResolution: 2.472→2.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HEIDIdata collection
REFMAC5.5.010refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.010phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4N4N

4n4n


Resolution: 2.472→49.95 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.585 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.881 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27289 7133 9.5 %RANDOM
Rwork0.22395 ---
all0.22859 68039 --
obs0.22859 68039 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.941 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2--2.49 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.472→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13284 0 1081 993 15358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9172.14520416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.46151670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87524.579653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.427152385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5261581
X-RAY DIFFRACTIONr_chiral_restr0.0610.21951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.03211548
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_it0.2011.58361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.369213460
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.40136598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.544.56956
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: 2.472→2.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 442 -
Rwork0.296 4265 -
obs--83.89 %

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