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- PDB-5v4t: Protein 84 with aldehyde deformylating oxygenase activity from Su... -

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Basic information

Entry
Database: PDB / ID: 5v4t
TitleProtein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (orthorhombic form)
Componentshypothetic aldehyde deformylating oxygenase
KeywordsOXIDOREDUCTASE / Ferritin / diiron
Function / homologyRibonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / metal ion binding / : / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 (orthorhombic form)
Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,1347
Polymers51,8362
Non-polymers2985
Water3,585199
1
A: hypothetic aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0363
Polymers25,9181
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetic aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0984
Polymers25,9181
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.466, 114.360, 64.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hypothetic 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% ethanol, 1.5 M NaCl

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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 S 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: 1.7→38.12 Å / Num. obs: 59271 / % possible obs: 99.7 % / Redundancy: 5.9 % / Net I/σ(I): 18.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UXG

5uxg


Resolution: 1.7→38.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.896 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21963 1752 3 %RANDOM
Rwork0.18888 ---
obs0.18978 57262 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20 Å2
2--1.11 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.7→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 14 199 3735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193605
X-RAY DIFFRACTIONr_bond_other_d0.0010.023557
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.9734844
X-RAY DIFFRACTIONr_angle_other_deg0.90638205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16724.253174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3761522
X-RAY DIFFRACTIONr_chiral_restr0.1190.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
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_it1.9671.9361694
X-RAY DIFFRACTIONr_mcbond_other1.9571.9351693
X-RAY DIFFRACTIONr_mcangle_it2.8992.8962114
X-RAY DIFFRACTIONr_mcangle_other2.92.8982115
X-RAY DIFFRACTIONr_scbond_it3.3432.3631911
X-RAY DIFFRACTIONr_scbond_other3.3432.3631911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.043.382731
X-RAY DIFFRACTIONr_long_range_B_refined6.07516.3744453
X-RAY DIFFRACTIONr_long_range_B_other6.07516.384454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 134 -
Rwork0.244 4077 -
obs--98.16 %

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