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- PDB-3al5: Crystal structure of Human TYW5 -

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Basic information

Entry
Database: PDB / ID: 3al5
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 / tRNA binding / iron ion binding / protein homodimerization activity / 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
tRNA wybutosine-synthesizing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.503 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 1.0Nov 24, 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 / 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 / _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)156,6796
Polymers156,6314
Non-polymers492
Water00
1
A: JmjC domain-containing protein C2orf60
B: JmjC domain-containing protein C2orf60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3403
Polymers78,3152
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-34 kcal/mol
Surface area27020 Å2
MethodPISA
2
C: JmjC domain-containing protein C2orf60
D: JmjC domain-containing protein C2orf60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3403
Polymers78,3152
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-33 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.942, 164.942, 105.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
11METMETchain B and resid 1:311 and (name C or name N or name O or name CA)BB1 - 31124 - 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
22GLNGLNchain A and resid 4:311 and (name C or name N or name O or name CA)AA4 - 31127 - 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.28 Å3/Da / Density % sol: 46.12 % / Mosaicity: 0.468 °
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: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 29, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 49257 / % possible obs: 97.6 % / Redundancy: 9 % / Rmerge(I) obs: 0.075 / Χ2: 1.357 / Net I/σ(I): 27.975
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.544.30.39223490.71194.9
2.54-2.594.60.37423510.707195.3
2.59-2.6450.35723800.757195.3
2.64-2.695.30.3523760.855195.9
2.69-2.755.40.3324170.818196.1
2.75-2.825.80.30923570.913196.2
2.82-2.896.20.28424230.934196.7
2.89-2.966.80.24624121.03197.1
2.96-3.057.30.22724191.114197
3.05-3.158.30.19424491.215197.9
3.15-3.268.90.17124711.268198.1
3.26-3.3910.10.13924511.37198.1
3.39-3.5511.40.11724781.517199
3.55-3.7311.90.10325181.649199.4
3.73-3.9712.40.08825021.735199.3
3.97-4.2712.70.07625081.781199.2
4.27-4.713.10.06825481.791199.4
4.7-5.3813.20.06325551.594199.4
5.38-6.7813.10.05725841.397199.3
6.78-5012.90.04127091.108197.8

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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: 2.503→50 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 0.3 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 2462 5 %RANDOM
Rwork0.2195 ---
obs0.2225 49227 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.326 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 184.68 Å2 / Biso mean: 77.6517 Å2 / Biso min: 18.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.9866 Å20 Å2-0 Å2
2--3.9866 Å20 Å2
3----7.9731 Å2
Refinement stepCycle: LAST / Resolution: 2.503→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9286 0 2 0 9288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099524
X-RAY DIFFRACTIONf_angle_d1.25312965
X-RAY DIFFRACTIONf_dihedral_angle_d20.1063303
X-RAY DIFFRACTIONf_chiral_restr0.0841425
X-RAY DIFFRACTIONf_plane_restr0.0051691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1136X-RAY DIFFRACTIONPOSITIONAL0.541
12C1136X-RAY DIFFRACTIONPOSITIONAL0.541
21D1208X-RAY DIFFRACTIONPOSITIONAL0.539
22A1208X-RAY DIFFRACTIONPOSITIONAL0.539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5034-2.55150.41891300.382246195
2.5515-2.60360.39151310.3553251095
2.6036-2.66020.38891330.3118251196
2.6602-2.72210.33761320.2991251196
2.7221-2.79010.33631330.2613252396
2.7901-2.86560.31581330.2469252196
2.8656-2.94990.29911350.2389256597
2.9499-3.0450.34011340.2477257097
3.045-3.15380.33571350.2396255998
3.1538-3.28010.31011370.2313259098
3.2801-3.42930.31281380.221263199
3.4293-3.610.30731380.2014260999
3.61-3.83610.21791390.192265399
3.8361-4.1320.27331390.1698264699
4.132-4.54740.22091400.1702266599
4.5474-5.20450.22681410.16242674100
5.2045-6.55330.28831440.211274599
6.5533-42.81920.24251500.2044282198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2148-0.4217-0.70733.1566-0.5672.9209-0.19040.6019-0.1760.55610.40680.58880.2795-0.5721-0.00070.37880.19450.16560.7939-0.00120.446-58.0874-70.297-32.7909
20.0282-0.0973-0.00730.43820.19260.5841-0.6863-0.0551-0.03810.39540.2937-0.03840.90450.28910.00040.94440.23320.31580.4550.00530.4733-63.7097-45.8736-8.5267
31.92320.15920.34671.92020.84942.7687-0.15030.14640.04860.06870.0739-0.0630.26810.470.00010.31630.10180.06120.26930.07560.3096-63.3937-17.5487-2.1283
40.0305-0.1191-0.05820.67510.14260.309-0.7662-0.0013-0.48550.6760.16240.1440.64870.4229-0.00040.78050.25480.23430.61810.0420.5042-58.9761-50.1683-11.0903
50.9510.511.09072.33410.37192.0084-0.3522-0.48760.299-0.71940.09260.1591-0.546-1.0967-0.00050.5926-0.1055-0.09140.8644-0.18630.5077-54.43667.15016.2091
60.03020.1303-0.15790.3373-0.12610.8345-0.2412-0.2474-0.2032-0.02710.1001-0.3657-1.0814-0.4577-0.00010.8125-0.05880.010.4308-0.10620.5719-60.003543.418-18.1128
72.2715-0.4625-0.43151.65870.88853.7502-0.0829-0.2999-0.0156-0.02820.0571-0.0582-0.22490.42090.00010.1431-0.08860.00470.21940.03670.232-62.04615.3257-26.5218
80.2284-0.2262-0.06750.6785-0.18270.6463-0.4417-0.07890.5583-0.73270.352-0.4986-1.20560.1806-0.00030.7274-0.14830.07130.5354-0.16590.5407-55.473147.3989-15.1522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:268A1 - 268
2X-RAY DIFFRACTION2CHAIN A AND RESID 269:399A269 - 399
3X-RAY DIFFRACTION3CHAIN B AND RESID 1:268B1 - 268
4X-RAY DIFFRACTION4CHAIN B AND RESID 269:399B269 - 399
5X-RAY DIFFRACTION5CHAIN C AND RESID 1:268C1 - 268
6X-RAY DIFFRACTION6CHAIN C AND RESID 269:399C269 - 399
7X-RAY DIFFRACTION7CHAIN D AND RESID 1:268D1 - 268
8X-RAY DIFFRACTION8CHAIN D AND RESID 269:399D269 - 399

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