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- PDB-6djt: Structure of TYW1 with a lysine-pyruvate adduct bound -

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Basic information

Entry
Database: PDB / ID: 6djt
TitleStructure of TYW1 with a lysine-pyruvate adduct bound
ComponentsS-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
KeywordsMETAL BINDING PROTEIN / S-Adenosylmethionine radical enzymes / tRNA biosynthetic enzyme
Function / homology
Function and homology information


tRNA 4-demethylwyosine synthase (AdoMet-dependent) / tRNA-4-demethylwyosine synthase activity / wybutosine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea / tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea / tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FE2/S3 CLUSTER / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGrell, T.A.J. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM72623 United States
National Science Foundation (NSF, United States)1122374 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1.
Authors: Grell, T.A.J. / Young, A.P. / Drennan, C.L. / Bandarian, V.
History
DepositionMay 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,52113
Polymers39,0111
Non-polymers1,51012
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.260, 80.109, 86.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / MjTYW1 / tRNA wyosine derivatives biosynthesis protein Taw1


Mass: 39011.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: taw1, MJ0257 / Production host: Escherichia coli (E. coli)
References: UniProt: Q57705, tRNA 4-demethylwyosine synthase (AdoMet-dependent)

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Non-polymers , 5 types, 203 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FS0 / FE2/S3 CLUSTER


Mass: 208.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2HS3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM potassium phosphate monobasic /sodium phosphate dibasic pH 6.2, 10% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 47373 / % possible obs: 94.1 % / Redundancy: 6.5 % / CC1/2: 0.942 / Rsym value: 0.063 / Net I/σ(I): 30.2
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3369 / CC1/2: 0.942 / Rsym value: 0.689 / % possible all: 68

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z2U

2z2u


Resolution: 1.64→48.314 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.1954 2382 5.04 %
Rwork0.1683 --
obs0.1697 47297 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→48.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 75 191 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072778
X-RAY DIFFRACTIONf_angle_d0.8413770
X-RAY DIFFRACTIONf_dihedral_angle_d16.4341716
X-RAY DIFFRACTIONf_chiral_restr0.055408
X-RAY DIFFRACTIONf_plane_restr0.005481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.67340.341910.28861791X-RAY DIFFRACTION64
1.6734-1.70980.24431200.26432041X-RAY DIFFRACTION74
1.7098-1.74960.30511190.23472212X-RAY DIFFRACTION81
1.7496-1.79340.25741300.22932464X-RAY DIFFRACTION89
1.7934-1.84180.24551320.21852636X-RAY DIFFRACTION94
1.8418-1.8960.2281430.20822723X-RAY DIFFRACTION98
1.896-1.95720.1991550.17642742X-RAY DIFFRACTION99
1.9572-2.02720.1941460.15622786X-RAY DIFFRACTION100
2.0272-2.10840.20721480.15392800X-RAY DIFFRACTION100
2.1084-2.20430.181420.15312764X-RAY DIFFRACTION100
2.2043-2.32050.20421500.15322803X-RAY DIFFRACTION100
2.3205-2.46590.18561480.15162792X-RAY DIFFRACTION100
2.4659-2.65630.18871420.15742814X-RAY DIFFRACTION100
2.6563-2.92360.18381460.15412836X-RAY DIFFRACTION100
2.9236-3.34650.16851580.14632830X-RAY DIFFRACTION100
3.3465-4.21590.15391460.14172887X-RAY DIFFRACTION100
4.2159-48.3350.21981660.19722994X-RAY DIFFRACTION100
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)
10.0155-0.0102-0.03210.1339-0.20920.41530.0485-0.01860.2680.1831-0.07050.5938-0.5910.0073-0.02130.31110.01860.07740.2344-0.03230.4178-7.07347.8936-20.0358
20.0648-0.03680.0640.0353-0.02740.0386-0.1112-0.13340.02940.1238-0.0735-0.0519-0.33020.1601-00.3182-0.0305-0.02350.25710.01050.224615.82698.5785-19.8008
30.0585-0.08870.01610.1072-0.033-0.01280.1122-0.120.16020.168-0.06390.2341-0.2130.077800.2467-0.01230.03090.2437-0.01250.23981.7070.473-20.0072
40.0711-0.0106-0.0020.1341-0.11390.0932-0.14580.01350.18390.28520.12910.2357-0.32790.049-0.0010.3958-0.04730.00060.3374-0.06990.4855-8.0868-3.1489-17.0134
50.0859-0.0782-0.06290.1416-0.06640.0838-0.02280.12040.1208-0.26660.097-0.0054-0.1553-0.040400.28660.0242-0.00040.21250.00540.28383.228111.0831-30.3504
60.3026-0.06060.05920.1315-0.13940.0628-0.03960.0520.0741-0.2747-0.01070.14420.07010.0482-0.00020.2648-0.00770.00570.2017-0.00690.1976.3730.3139-28.3962
70.67650.16010.32950.48540.07520.3296-0.0125-0.0619-0.0625-0.002-0.02010.03390.34380.09540.00010.26790.01030.03760.2-0.00210.20724.1852-13.0746-12.3527
80.90690.63540.32510.4828-0.0710.8886-0.0018-0.07820.04950.1414-0.0755-0.0211-0.02640.1616-0.00010.22180.0393-0.00410.22860.00810.186516.124-5.5103-6.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 154 )
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 214 )
8X-RAY DIFFRACTION8chain 'A' and (resid 215 through 311 )

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