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- PDB-6x6u: WOR5 from Pyrococcus furiosus, taurine-bound -

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Basic information

Entry
Database: PDB / ID: 6x6u
TitleWOR5 from Pyrococcus furiosus, taurine-bound
Components
  • Formaldehyde:ferredoxin oxidoreductase wor5
  • Oxidoreductase, Fe-S subunit
KeywordsCYTOSOLIC 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 / 2-AMINOETHANESULFONIC ACID / Oxidoreductase, Fe-S subunit / aldehyde ferredoxin oxidoreductase
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.944 Å
AuthorsLanzilotta, W.N. / Mathew, L.G.
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 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 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)184,23832
Polymers177,5404
Non-polymers6,69928
Water15,277848
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22440 Å2
ΔGint-435 kcal/mol
Surface area46700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.148, 127.501, 140.712
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: 69851.930 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: 18917.922 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, 876 molecules

#3: Chemical ChemComp-PTE / TUNGSTOPTERIN COFACTOR


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


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
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: 1.944→50 Å / Num. obs: 300670 / % possible obs: 94.7 % / Redundancy: 15 % / CC1/2: 0.986 / CC star: 0.996 / Rpim(I) all: 0.069 / Rrim(I) all: 0.293 / Net I/σ(I): 16.42
Reflection shellResolution: 2.02→2.1 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 27757 / CC1/2: 0.307 / CC star: 0.685 / Rpim(I) all: 0.318 / Rrim(I) all: 0.875 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.944→38.162 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 2006 1.28 %
Rwork0.1704 --
obs0.1707 156696 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.944→38.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12528 0 56 848 13432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312938
X-RAY DIFFRACTIONf_angle_d1.87717615
X-RAY DIFFRACTIONf_dihedral_angle_d6.410449
X-RAY DIFFRACTIONf_chiral_restr0.0661913
X-RAY DIFFRACTIONf_plane_restr0.0082209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.944-1.99240.3028980.29436976X-RAY DIFFRACTION61
1.9924-2.04630.28091300.26489920X-RAY DIFFRACTION86
2.0463-2.10650.29821380.23110586X-RAY DIFFRACTION92
2.1065-2.17450.24481420.209411062X-RAY DIFFRACTION96
2.1745-2.25220.23291500.198211313X-RAY DIFFRACTION98
2.2522-2.34240.21021430.18811405X-RAY DIFFRACTION98
2.3424-2.44890.23131530.182411526X-RAY DIFFRACTION99
2.4489-2.5780.21891470.176711481X-RAY DIFFRACTION99
2.578-2.73950.20711510.173211592X-RAY DIFFRACTION100
2.7395-2.95090.19591460.168511633X-RAY DIFFRACTION100
2.9509-3.24780.18381560.169811663X-RAY DIFFRACTION100
3.2478-3.71740.16351470.158211714X-RAY DIFFRACTION100
3.7174-4.68220.13311510.128911774X-RAY DIFFRACTION100
4.6822-38.1620.19261540.145812045X-RAY DIFFRACTION99

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