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- PDB-6h5l: Kuenenia stuttgartiensis reducing HAO-like protein complex Kustc0... -

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Basic information

Entry
Database: PDB / ID: 6h5l
TitleKuenenia stuttgartiensis reducing HAO-like protein complex Kustc0457/Kustc0458
Components
  • Conserved hypothetical cytochrome protein
  • Similar to hydroxylamine oxidoreductase
KeywordsOXIDOREDUCTASE / reductase / anammox
Function / homology
Function and homology information


hydroxylamine oxidase / anammoxosome / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Seven times multi-haem cytochrome CxxCH / : / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / Putative hydroxylamine oxidoreductase hao / Similar to hydroxylamine oxidoreductase / C-type diheme-containing protein
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 Å
AuthorsDietl, A. / Maalcke, W. / Barends, T.R.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway.
Authors: Dietl, A. / Maalcke, W.J. / Ferousi, C. / Jetten, M.S.M. / Kartal, B. / Barends, T.R.M.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Similar to hydroxylamine oxidoreductase
B: Conserved hypothetical cytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,44212
Polymers85,2572
Non-polymers6,18510
Water3,549197
1
A: Similar to hydroxylamine oxidoreductase
B: Conserved hypothetical cytochrome protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)548,65272
Polymers511,54212
Non-polymers37,11060
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area129340 Å2
ΔGint-1731 kcal/mol
Surface area147030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.200, 140.200, 262.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

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Components

#1: Protein Similar to hydroxylamine oxidoreductase


Mass: 59818.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HAO-like reductase / Source: (natural) Kuenenia stuttgartiensis (bacteria)
References: UniProt: Q1PVE0, UniProt: A0A2C9CG41*PLUS, hydroxylamine oxidase
#2: Protein Conserved hypothetical cytochrome protein


Mass: 25438.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PVE1
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M ammonium sulfate, 1% Tween-20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2011 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→60 Å / Num. obs: 29078 / % possible obs: 94.4 % / Redundancy: 2.9 % / Rrim(I) all: 0.113 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4707 / Rrim(I) all: 0.393 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→59.143 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.07
RfactorNum. reflection% reflection
Rfree0.2336 1469 5.05 %
Rwork0.1894 --
obs0.1917 29078 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→59.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 430 197 6471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036515
X-RAY DIFFRACTIONf_angle_d0.7128972
X-RAY DIFFRACTIONf_dihedral_angle_d17.4493670
X-RAY DIFFRACTIONf_chiral_restr0.04825
X-RAY DIFFRACTIONf_plane_restr0.0041132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6930.38671280.32352606X-RAY DIFFRACTION90
2.693-2.80080.28981420.24382853X-RAY DIFFRACTION99
2.8008-2.92830.25951620.22182846X-RAY DIFFRACTION98
2.9283-3.08260.28011270.21542844X-RAY DIFFRACTION98
3.0826-3.27580.30441740.21492809X-RAY DIFFRACTION97
3.2758-3.52870.23341550.19372800X-RAY DIFFRACTION97
3.5287-3.88370.21061530.17022764X-RAY DIFFRACTION95
3.8837-4.44550.18331480.15272768X-RAY DIFFRACTION94
4.4455-5.60020.19791520.14962705X-RAY DIFFRACTION92
5.6002-59.1580.17661280.15782614X-RAY DIFFRACTION85

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