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- PDB-4n4l: Kuenenia stuttgartiensis hydroxylamine oxidoreductase soaked in h... -

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Basic information

Entry
Database: PDB / ID: 4n4l
TitleKuenenia stuttgartiensis hydroxylamine oxidoreductase soaked in hydrazine
Componentshydroxylamine oxidoreductase
KeywordsOXIDOREDUCTASE / C-type cytochrome
Function / homology
Function and homology information


hydroxylamine oxidase / anaerobic respiration, using ammonium as electron donor / hydroxylamine oxidoreductase activity / anammoxosome / protein homotrimerization / nitric oxide biosynthetic process / heme binding / metal ion binding / identical protein binding
Similarity search - Function
Hydroxylamine oxidase / Seven times multi-haem cytochrome CxxCH / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / Chem-HG1 / hydrazine / PHOSPHATE ION / Hydroxylamine oxidoreductase
Similarity search - Component
Biological speciesCandidatus Kuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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_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_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_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,71622
Polymers56,5441
Non-polymers6,17221
Water7,512417
1
A: hydroxylamine oxidoreductase
hetero molecules

A: hydroxylamine oxidoreductase
hetero molecules

A: hydroxylamine oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,14766
Polymers169,6313
Non-polymers18,51663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area58970 Å2
ΔGint-728 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.000, 130.000, 130.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-603-

PO4

21A-603-

PO4

31A-888-

HOH

DetailsCovalent trimer confirmed by SDS-PAGE, analytical ultracentrifugation, and gel filtration

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Components

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Protein , 1 types, 1 molecules A

#1: Protein hydroxylamine oxidoreductase / / Similar to hydroxylamine oxidoreductase hao


Mass: 56543.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Candidatus Kuenenia stuttgartiensis (bacteria)
References: UniProt: Q1PX48, hydroxylamine oxidase

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Non-polymers , 6 types, 438 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HZN / hydrazine / Hydrazine


Mass: 32.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N2
#5: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-HG1 / 1-[(4-cyclohexylbutanoyl)(2-hydroxyethyl)amino]-1-deoxy-D-glucitol / C-HEGA-10


Mass: 377.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H35NO7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.3 M ammonium sulfate, 0.05-0.10 M sodium phosphate, pH 7.4, detergent additive cyclohexylbutanoyl-N-hydroxyethylglucamide (C-HEGA-10), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→46 Å / Num. all: 54927 / Num. obs: 54927 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.464 / % possible all: 99.9

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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 4N4J
Resolution: 1.9→45.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.832 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 2786 4.8 %RANDOM
Rwork0.1478 ---
all0.14852 54927 --
obs0.14852 54927 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: 14.714 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 406 417 4763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224564
X-RAY DIFFRACTIONr_bond_other_d0.0010.023038
X-RAY DIFFRACTIONr_angle_refined_deg1.0862.1596226
X-RAY DIFFRACTIONr_angle_other_deg0.8193.0047276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40223.7200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67715668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0325009
X-RAY DIFFRACTIONr_gen_planes_other0.0090.026884
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_it0.3341.52482
X-RAY DIFFRACTIONr_mcbond_other0.0781.51020
X-RAY DIFFRACTIONr_mcangle_it0.64523979
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.98532081
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4954.52246
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 213 -
Rwork0.185 3986 -
obs--100 %

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