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- PDB-3al6: Crystal structure of Human TYW5 -

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Basic information

Entry
Database: PDB / ID: 3al6
TitleCrystal structure of Human TYW5
ComponentsJmjC domain-containing protein C2orf60
KeywordsUNKNOWN FUNCTION / tRNA modification enzyme
Function / homology
Function and homology information


tRNAPhe (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase / tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase activity / Synthesis of wybutosine at G37 of tRNA(Phe) / wybutosine biosynthetic process / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / tRNA binding / iron ion binding / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #1470 / Cupin-like domain 8 / Cupin-like domain / Helix Hairpins / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Helix non-globular / Special ...Helix Hairpins - #1470 / Cupin-like domain 8 / Cupin-like domain / Helix Hairpins / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Helix non-globular / Special / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / tRNA wybutosine-synthesizing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKato, M. / Araiso, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.
Authors: Kato, M. / Araiso, Y. / Noma, A. / Nagao, A. / Suzuki, T. / Ishitani, R. / Nureki, O.
History
DepositionJul 26, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein C2orf60
B: JmjC domain-containing protein C2orf60
C: JmjC domain-containing protein C2orf60
D: JmjC domain-containing protein C2orf60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,15810
Polymers156,6314
Non-polymers5276
Water00
1
A: JmjC domain-containing protein C2orf60
B: JmjC domain-containing protein C2orf60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5795
Polymers78,3152
Non-polymers2633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-34 kcal/mol
Surface area26250 Å2
MethodPISA
2
C: JmjC domain-containing protein C2orf60
D: JmjC domain-containing protein C2orf60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5795
Polymers78,3152
Non-polymers2633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-36 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.871, 165.871, 105.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12D
22A

NCS domain segments:

Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNchain B and resid 4:311 and (name C or name N or name O or name CA)BB4 - 31127 - 334
21LEULEUchain C and resid 6:311 and (name C or name N or name O or name CA)CC6 - 31129 - 334
12GLNGLNchain D and resid 4:311 and (name C or name N or name O or name CA)DD4 - 31127 - 334
22HISHISchain A and resid 5:311 and (name C or name N or name O or name CA)AA5 - 31128 - 334

NCS ensembles :
ID
1
2

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Components

#1: Protein
JmjC domain-containing protein C2orf60 / hTYW5


Mass: 39157.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2orf60 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A2RUC4
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5

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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: 2.33 Å3/Da / Density % sol: 47.13 % / Mosaicity: 0.419 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM potassium thiocyanate, 10% (w/v) PEG3350, pH 8.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.48505 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48505 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 36950 / % possible obs: 99.6 % / Redundancy: 19 % / Rmerge(I) obs: 0.082 / Χ2: 2.651 / Net I/σ(I): 56.444
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.855.70.4817760.84198.1
2.85-2.970.45918060.811199.1
2.9-2.969.10.43518160.897199.8
2.96-3.0212.10.41618260.9311100
3.02-3.0814.70.39218230.9611100
3.08-3.1516.30.34118061.0721100
3.15-3.2317.40.30718461.1991100
3.23-3.3218.50.26818391.3431100
3.32-3.4219.80.21518341.558199.9
3.42-3.5321.40.19618301.9891100
3.53-3.65220.14718392.081199.9
3.65-3.822.60.13718442.415199.9
3.8-3.97230.11118312.737199.9
3.97-4.1824.10.08718543.0331100
4.18-4.4424.70.07518653.364199.9
4.44-4.79250.06418663.711199.9
4.79-5.2725.30.06318683.8471100
5.27-6.0324.50.06618944.255199.9
6.03-7.5924.20.06219334.353199.9
7.59-50220.0519544.123195.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→49.017 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0.15 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2954 1840 5 %RANDOM
Rwork0.2399 ---
obs0.2427 36782 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.555 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 194.21 Å2 / Biso mean: 86.8914 Å2 / Biso min: 36.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.9379 Å20 Å2-0 Å2
2--2.9379 Å20 Å2
3----5.8757 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9013 0 24 0 9037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019267
X-RAY DIFFRACTIONf_angle_d1.3612643
X-RAY DIFFRACTIONf_dihedral_angle_d20.0923130
X-RAY DIFFRACTIONf_chiral_restr0.0861408
X-RAY DIFFRACTIONf_plane_restr0.0061644
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1092X-RAY DIFFRACTIONPOSITIONAL
12C1092X-RAY DIFFRACTIONPOSITIONAL0.673
21D1196X-RAY DIFFRACTIONPOSITIONAL
22A1196X-RAY DIFFRACTIONPOSITIONAL0.526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.87570.37041370.3344259998
2.8757-2.96030.3761390.30342649100
2.9603-3.05580.35231390.28352641100
3.0558-3.1650.30011410.27182678100
3.165-3.29170.33371400.24332656100
3.2917-3.44150.28061400.23852667100
3.4415-3.62290.30021410.22342677100
3.6229-3.84980.28451420.23242688100
3.8498-4.14690.29661400.22142686100
4.1469-4.5640.25511430.20942702100
4.564-5.22370.25411430.20182716100
5.2237-6.57890.29911460.24052766100
6.5789-49.02490.30061490.2414281797

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