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- PDB-6t5e: Hydroxylamine Oxidoreductase from Brocadia fulgida -

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Basic information

Entry
Database: PDB / ID: 6t5e
TitleHydroxylamine Oxidoreductase from Brocadia fulgida
ComponentsHydroxylamine oxidoreductase-like protein
KeywordsOXIDOREDUCTASE / redox / anammox / anaerobic ammonium oxidation
Function / homology: / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / HEME C / Hydroxylamine oxidoreductase-like protein
Function and homology information
Biological speciesCandidatus Brocadia fulgida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAkram, M. / Dietl, A. / Mueller, M. / Barends, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council724362 Germany
CitationJournal: Biopolymers / Year: 2021
Title: Purification of the key enzyme complexes of the anammox pathway from DEMON sludge.
Authors: Akram, M. / Dietl, A. / Muller, M. / Barends, T.R.M.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 7, 2021Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_validate_symm_contact / struct_conn
Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Hydroxylamine oxidoreductase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,61611
Polymers56,4751
Non-polymers5,14010
Water0
1
A: Hydroxylamine oxidoreductase-like protein
hetero molecules

A: Hydroxylamine oxidoreductase-like protein
hetero molecules

A: Hydroxylamine oxidoreductase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,84733
Polymers169,4263
Non-polymers15,42030
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area49190 Å2
ΔGint-732 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.560, 124.560, 124.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Hydroxylamine oxidoreductase-like protein


Mass: 56475.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidatus Brocadia fulgida (bacteria) / References: UniProt: A0A0M2UZI7
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0 M Lithium chloride, 0.1 M Tris pH 8.5 10% w/v PEG 6K, final pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→88.08 Å / Num. obs: 18802 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.184 / Net I/σ(I): 11.3
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.56 / Num. unique obs: 1404 / CC1/2: 0.653 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4J

4n4j


Resolution: 3.3→44.08 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 27.746 / SU ML: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 455 4.6 %RANDOM
Rwork0.2204 ---
obs0.2224 9487 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.06 Å2 / Biso mean: 96.313 Å2 / Biso min: 76.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.3→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 354 0 3841
Biso mean--96.74 --
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134033
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.85520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2465436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7222.041196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78915579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7951521
X-RAY DIFFRACTIONr_chiral_restr0.0620.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0363217
LS refinement shellResolution: 3.301→3.387 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 30 -
Rwork0.317 694 -
all-724 -
obs--100 %

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