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- PDB-5uxg: Protein 84 with aldehyde deformylating oxygenase activity from Su... -

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Basic information

Entry
Database: PDB / ID: 5uxg
TitleProtein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)
Componentsaldehyde deformylating oxygenase
KeywordsLYASE / decarbonylase / iron / ferritin
Function / homologyRibonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / PHOSPHATE ION / Ferritin-like domain-containing protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsWilson, D.K. / Mak, W.S. / Siegel, J.B.
CitationJournal: To Be Published
Title: Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)
Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aldehyde deformylating oxygenase
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1215
Polymers51,8362
Non-polymers2853
Water3,819212
1
A: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1083
Polymers25,9181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0132
Polymers25,9181
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.536, 64.849, 71.299
Angle α, β, γ (deg.)90.00, 116.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein aldehyde deformylating oxygenase


Mass: 25917.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST1620, STK_16200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q970H5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Potassium phosphate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.72→63.61 Å / Num. obs: 55207 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.7 / % possible all: 57

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: theoretical

Resolution: 1.72→63.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.494 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22341 1647 3.1 %RANDOM
Rwork0.1952 ---
obs0.1961 51501 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.536 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.26 Å2
2---0.29 Å20 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.72→63.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 15 212 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193601
X-RAY DIFFRACTIONr_bond_other_d0.0010.023538
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9744846
X-RAY DIFFRACTIONr_angle_other_deg0.8638162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64124.253174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
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_it1.8291.9291690
X-RAY DIFFRACTIONr_mcbond_other1.8091.9281689
X-RAY DIFFRACTIONr_mcangle_it2.6332.8882109
X-RAY DIFFRACTIONr_mcangle_other2.6342.8882110
X-RAY DIFFRACTIONr_scbond_it3.1252.371911
X-RAY DIFFRACTIONr_scbond_other3.1232.361900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9253.382720
X-RAY DIFFRACTIONr_long_range_B_refined6.11616.3294445
X-RAY DIFFRACTIONr_long_range_B_other6.06916.1454387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 72 -
Rwork0.212 2625 -
obs--66.56 %

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