[English] 日本語
Yorodumi
- PDB-4ycp: E. coli dihydrouridine synthase C (DusC) in complex with tRNATrp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ycp
TitleE. coli dihydrouridine synthase C (DusC) in complex with tRNATrp
Components
  • tRNA-dihydrouridine synthase C
  • tRNATrp
KeywordsOxidoreductase/RNA / tRNA modification / oxidoreductase-RNA complex
Function / homology
Function and homology information


tRNA-dihydrouridine16 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I ...Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / RNA / RNA (> 10) / tRNA-dihydrouridine(16) synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsByrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
Funding support United Kingdom, Russian Federation, 3items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
RFBR13-04-40212-H comfi Russian Federation
RSF14-34-00023 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.
Authors: Byrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jan 10, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA-dihydrouridine synthase C
B: tRNATrp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9156
Polymers60,2422
Non-polymers6734
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-57 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.516, 98.516, 231.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

-
Components

-
Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein tRNA-dihydrouridine synthase C / DusC


Mass: 35779.992 Da / Num. of mol.: 1 / Fragment: UNP residues 1-315 / Mutation: C98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dusC, yohI, b2140, JW2128 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33371, Oxidoreductases
#2: RNA chain tRNATrp


Mass: 24462.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: GenBank: 731469900

-
Non-polymers , 4 types, 56 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Li2SO4 26% PEG 2K MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.55→49.26 Å / Num. obs: 22329 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 44.936 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bfa

4bfa


Resolution: 2.55→49.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.303 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1127 5 %RANDOM
Rwork0.2081 ---
obs0.2095 21202 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.39 Å2 / Biso mean: 49.616 Å2 / Biso min: 24.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å20 Å2
2---0.52 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 2.55→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 1287 42 52 3779
Biso mean--46.32 38.73 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.00639260.016
X-RAY DIFFRACTIONr_bond_other_d0.00229740.02
X-RAY DIFFRACTIONr_angle_refined_deg1.00356211.689
X-RAY DIFFRACTIONr_angle_other_deg1.04468843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5783214.86
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22211223.839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99440915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9982115
X-RAY DIFFRACTIONr_chiral_restr0.0616200.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00436240.02
X-RAY DIFFRACTIONr_gen_planes_other0.0018840.02
X-RAY DIFFRACTIONr_mcbond_it0.31812302.673
X-RAY DIFFRACTIONr_mcbond_other0.31812292.673
X-RAY DIFFRACTIONr_mcangle_it0.56215344.008
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 93 -
Rwork0.321 1534 -
all-1627 -
obs--99.69 %
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)
12.1395-0.39080.40312.84110.47742.963-0.0587-0.23610.03-0.04430.0155-0.11150.2076-0.20140.04320.072-0.0670.00370.198-0.00880.006327.7179-42.2182-4.3455
21.9897-0.15890.19252.11010.65643.2542-0.0419-0.2047-0.22090.15120.0872-0.11570.62970.2348-0.04530.1714-0.02390.00750.2080.0130.040436.3254-50.713-7.3043
33.4707-1.406-0.90492.06120.52172.6492-0.0985-0.18960.2570.08540.1658-0.3367-0.30280.2638-0.06730.1054-0.084-0.06280.2355-0.03460.12739.2024-32.1907-0.5191
43.8271.1705-1.27716.0735-1.16122.5255-0.0031-0.17650.42850.50970.1320.2966-0.6593-0.619-0.1290.25050.13660.01270.413-0.05040.057817.7742-30.413310.2686
50.17260.7768-0.05236.47010.95570.5126-0.0349-0.111-0.12370.2132-0.112-0.29440.21810.12140.1470.303-0.1055-0.00340.35620.07920.182625.105-55.83312.3847
65.3225-0.4140.09063.42641.06581.05070.07790.6801-0.1106-0.3552-0.34020.8822-0.1247-0.45280.26230.4459-0.074-0.11590.4717-0.04410.31249.6601-66.0161-1.413
73.1931-2.7799-0.73613.72682.17961.9877-0.08390.23890.4833-0.2745-0.1342-0.1829-0.41610.00160.21820.6845-0.0112-0.10510.5973-0.16850.62836.7879-70.9474-8.5474
817.52463.303316.57530.63613.103815.7174-0.5703-1.08670.8746-0.0231-0.22770.1784-0.6897-1.04780.7980.63150.0529-0.03750.4893-0.12870.513811.8122-58.81885.8729
90.3160.9911-0.36375.4445-3.61593.48620.0593-0.0733-0.15520.5085-0.1136-0.33310.0297-0.04450.05420.4918-0.04480.01850.3552-0.0180.132525.4969-52.594325.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 45
2X-RAY DIFFRACTION2A46 - 163
3X-RAY DIFFRACTION3A164 - 257
4X-RAY DIFFRACTION4A258 - 315
5X-RAY DIFFRACTION5B5 - 21
6X-RAY DIFFRACTION6B22 - 32
7X-RAY DIFFRACTION7B36 - 42
8X-RAY DIFFRACTION8B43 - 47
9X-RAY DIFFRACTION9B48 - 69

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more