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- PDB-6x1o: WOR5 from Pyrococcus furiosus, as crystallized -

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Basic information

Entry
Database: PDB / ID: 6x1o
TitleWOR5 from Pyrococcus furiosus, as crystallized
Components
  • Formaldehyde:ferredoxin oxidoreductase wor5
  • Oxidoreductase, Fe-S subunit
KeywordsOXIDOREDUCTASE / aldehyde oxidoreductase / hyperthermophilic / tungstopterin / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


aldehyde ferredoxin oxidoreductase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding
Similarity search - Function
Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / 4Fe-4S binding domain ...Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / 4Fe-4S binding domain / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
PHOSPHATE ION / TUNGSTOPTERIN COFACTOR / IRON/SULFUR CLUSTER / (1R)-1-hydroxybutane-1-sulfonic acid / Oxidoreductase, Fe-S subunit / aldehyde ferredoxin oxidoreductase
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.094 Å
AuthorsMathew, L.G. / Lanzilotta, W.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2022
Title: An unprecedented function for a tungsten-containing oxidoreductase.
Authors: Mathew, L.G. / Haja, D.K. / Pritchett, C. / McCormick, W. / Zeineddine, R. / Fontenot, L.S. / Rivera, M.E. / Glushka, J. / Adams, M.W.W. / Lanzilotta, W.N.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formaldehyde:ferredoxin oxidoreductase wor5
B: Oxidoreductase, Fe-S subunit
C: Formaldehyde:ferredoxin oxidoreductase wor5
D: Oxidoreductase, Fe-S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,17526
Polymers175,9284
Non-polymers6,24722
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20310 Å2
ΔGint-377 kcal/mol
Surface area46070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.092, 126.821, 141.289
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, 4 molecules ACBD

#1: Protein Formaldehyde:ferredoxin oxidoreductase wor5


Mass: 69965.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06635 / Production host: Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6V2C3
#2: Protein Oxidoreductase, Fe-S subunit


Mass: 17998.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06630 / Production host: Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6U881

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Non-polymers , 7 types, 237 molecules

#3: Chemical ChemComp-UKM / (1R)-1-hydroxybutane-1-sulfonic acid


Mass: 154.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4S
#4: Chemical ChemComp-PTE / TUNGSTOPTERIN COFACTOR


Mass: 1031.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29MgN10O14P2S4W
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 298 K / Method: counter-diffusion / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.094→47.19 Å / Num. obs: 498042 / % possible obs: 99.08 % / Redundancy: 12.1 % / CC1/2: 0.994 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Χ2: 1.019 / Net I/σ(I): 15.575
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.346 / Num. unique obs: 24417 / CC1/2: 0.946 / Rpim(I) all: 0.213 / Rrim(I) all: 0.738 / Χ2: 0.402

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.094→47.189 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 3873 1.56 %
Rwork0.1785 --
obs0.1789 249021 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.094→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12536 0 34 215 12785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212897
X-RAY DIFFRACTIONf_angle_d1.71717538
X-RAY DIFFRACTIONf_dihedral_angle_d6.6358949
X-RAY DIFFRACTIONf_chiral_restr0.0681904
X-RAY DIFFRACTIONf_plane_restr0.0072198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.094-2.11950.29661350.29637834X-RAY DIFFRACTION88
2.1195-2.14630.27861270.26788771X-RAY DIFFRACTION99
2.1463-2.17460.27431310.24918861X-RAY DIFFRACTION99
2.1746-2.20430.32031420.24148767X-RAY DIFFRACTION99
2.2043-2.23580.2361430.22728815X-RAY DIFFRACTION99
2.2358-2.26920.27281350.22398775X-RAY DIFFRACTION99
2.2692-2.30470.23611570.21888734X-RAY DIFFRACTION99
2.3047-2.34240.2511140.21248764X-RAY DIFFRACTION99
2.3424-2.38280.27381580.21988807X-RAY DIFFRACTION99
2.3828-2.42620.25711420.21258785X-RAY DIFFRACTION99
2.4262-2.47280.23771320.21058766X-RAY DIFFRACTION99
2.4728-2.52330.25221340.2078830X-RAY DIFFRACTION99
2.5233-2.57820.25481330.21358634X-RAY DIFFRACTION99
2.5782-2.63810.24651560.2088923X-RAY DIFFRACTION100
2.6381-2.70410.22681310.19848764X-RAY DIFFRACTION100
2.7041-2.77720.27461350.20188815X-RAY DIFFRACTION100
2.7772-2.85890.22841410.19948857X-RAY DIFFRACTION100
2.8589-2.95120.2451430.20468845X-RAY DIFFRACTION100
2.9512-3.05660.25661380.20288812X-RAY DIFFRACTION100
3.0566-3.1790.2121320.20328822X-RAY DIFFRACTION100
3.179-3.32360.23621510.19278816X-RAY DIFFRACTION100
3.3236-3.49880.21421310.1848778X-RAY DIFFRACTION99
3.4988-3.7180.20981310.17448682X-RAY DIFFRACTION98
3.718-4.00490.18781410.15178756X-RAY DIFFRACTION99
4.0049-4.40760.16921320.13778836X-RAY DIFFRACTION100
4.4076-5.04480.14461500.12838848X-RAY DIFFRACTION100
5.0448-6.35350.1421310.13988803X-RAY DIFFRACTION100
6.3535-47.1890.13461470.138648X-RAY DIFFRACTION98

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