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- PDB-5ux1: Protein 43 with aldehyde deformylating oxygenase activity from Sy... -

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Basic information

Entry
Database: PDB / ID: 5ux1
TitleProtein 43 with aldehyde deformylating oxygenase activity from Synechococcus
ComponentstRNA-(MS(2)IO(6)A)-hydroxylase-like
KeywordsLYASE / decarbonylase / iron / ferritin
Function / homology
Function and homology information


tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity
Similarity search - Function
tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / tRNA-(MS(2)IO(6)A)-hydroxylase-like
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsWilson, D.K. / Mak, W.S. / Siegel, J.B.
CitationJournal: To Be Published
Title: Protein 43 with aldehyde deformylating oxygenase activity from Synechococcus
Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: tRNA-(MS(2)IO(6)A)-hydroxylase-like
B: tRNA-(MS(2)IO(6)A)-hydroxylase-like
C: tRNA-(MS(2)IO(6)A)-hydroxylase-like
D: tRNA-(MS(2)IO(6)A)-hydroxylase-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,87312
Polymers106,4264
Non-polymers4478
Water9,548530
1
A: tRNA-(MS(2)IO(6)A)-hydroxylase-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7183
Polymers26,6061
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA-(MS(2)IO(6)A)-hydroxylase-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7183
Polymers26,6061
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA-(MS(2)IO(6)A)-hydroxylase-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7183
Polymers26,6061
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tRNA-(MS(2)IO(6)A)-hydroxylase-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7183
Polymers26,6061
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.342, 78.274, 83.734
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA-(MS(2)IO(6)A)-hydroxylase-like / aldehyde deformylating oxygenase


Mass: 26606.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9605) (bacteria)
Strain: CC9605 / Gene: Syncc9605_0503 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AMA5
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 3350, 140 mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.5→81.5 Å / Num. obs: 143854 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 19.5
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.3 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→81.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.519 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21473 3619 2.5 %RANDOM
Rwork0.19167 ---
obs0.19226 140203 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.875 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å2-0.22 Å2
2--0.25 Å2-0 Å2
3---1.2 Å2
Refinement stepCycle: 1 / Resolution: 1.5→81.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6367 0 8 530 6905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196515
X-RAY DIFFRACTIONr_bond_other_d0.0010.026266
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9748833
X-RAY DIFFRACTIONr_angle_other_deg0.801314385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5415797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87822.675314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4711571
X-RAY DIFFRACTIONr_chiral_restr0.0770.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021503
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_it1.292.0623200
X-RAY DIFFRACTIONr_mcbond_other1.2892.0613199
X-RAY DIFFRACTIONr_mcangle_it1.9353.0863993
X-RAY DIFFRACTIONr_mcangle_other1.9353.0873994
X-RAY DIFFRACTIONr_scbond_it2.2352.3893315
X-RAY DIFFRACTIONr_scbond_other2.2342.393316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.463.4844841
X-RAY DIFFRACTIONr_long_range_B_refined4.73317.5077996
X-RAY DIFFRACTIONr_long_range_B_other4.63817.2067783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 264 -
Rwork0.279 10134 -
obs--97.1 %

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