[English] 日本語
Yorodumi
- PDB-3wc2: Crystal structure of C. albicans tRNA(His) guanylyltransferase (T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wc2
TitleCrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)
Components
  • 76mer-tRNA
  • Likely histidyl tRNA-specific guanylyltransferase
KeywordsTRANSFERASE/RNA / TRANSFERASE-RNA complex
Function / homologytRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / RNA / RNA (> 10) / :
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.641 Å
AuthorsNakamura, A. / Nemoto, T. / Sonoda, T. / Yamashita, K. / Tanaka, I. / Yao, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of reverse nucleotide polymerization
Authors: Nakamura, A. / Nemoto, T. / Heinemann, I.U. / Yamashita, K. / Sonoda, T. / Komoda, K. / Tanaka, I. / Soll, D. / Yao, M.
History
DepositionMay 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Likely histidyl tRNA-specific guanylyltransferase
B: Likely histidyl tRNA-specific guanylyltransferase
C: Likely histidyl tRNA-specific guanylyltransferase
D: Likely histidyl tRNA-specific guanylyltransferase
P: 76mer-tRNA
Q: 76mer-tRNA


Theoretical massNumber of molelcules
Total (without water)179,7806
Polymers179,7806
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-112 kcal/mol
Surface area60890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.740, 96.740, 299.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Likely histidyl tRNA-specific guanylyltransferase


Mass: 32689.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: CaO19.7063, CAWG_05412, orf19.7063, THG1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5AFK5
#2: RNA chain 76mer-tRNA


Mass: 24511.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcription

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Bis-Tris propan, CaCl2, PEG 3350, pH 6.0, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.64→48.711 Å / Num. obs: 18933 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 125.88 Å2 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.113 / Net I/σ(I): 16.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.64-3.860.7141.22.0528390300629491.1898.1
3.86-4.130.8840.6893.6828310279327930.726100
4.13-4.450.960.397.0226260265526550.411100
4.45-4.870.9890.19612.8522468243124310.207100
4.87-5.440.9920.14517.0320686223422340.153100
5.44-6.270.9950.11521.1619851196419640.121100
6.27-7.650.9980.06932.3216449171717170.073100
7.65-10.690.9990.0447.6611244136313630.042100
10.690.9990.03260.0268818528270.03497.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WBZ

3wbz


Resolution: 3.641→38.09 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7663 / SU ML: 0.53 / Phase error: 29.43
RfactorNum. reflection% reflection
Rfree0.2875 1333 7.04 %
Rwork0.2529 --
obs0.2552 18926 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 280.99 Å2 / Biso mean: 104.9006 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: LAST / Resolution: 3.641→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8128 3146 0 0 11274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411872
X-RAY DIFFRACTIONf_angle_d0.76116758
X-RAY DIFFRACTIONf_chiral_restr0.0351887
X-RAY DIFFRACTIONf_plane_restr0.0031563
X-RAY DIFFRACTIONf_dihedral_angle_d14.0934874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.641-3.77140.34221170.33221670178797
3.7714-3.92230.34431500.321917121862100
3.9223-4.10060.32921350.309117321867100
4.1006-4.31650.3641230.294217361859100
4.3165-4.58650.28231260.261417661892100
4.5865-4.940.30391420.245717361878100
4.94-5.43580.27071170.254817621879100
5.4358-6.21950.3341300.265917901920100
6.2195-7.82470.25521580.265817681926100
7.8247-38.09220.24991350.207419212056100
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)
10.0891-0.0755-0.09510.1550.0250.138-0.2152-0.2094-0.1208-0.19250.1868-0.22630.23510.18020.10010.06820.79030.5270.50520.0760.232852.3118-41.9598-16.7965
20.0793-0.0284-0.00410.0162-0.01540.0266-0.2831-0.0038-0.283-0.18350.0275-0.1170.18540.0083-0.09320.81810.35261.0460.0511-0.1080.402328.5425-60.8517-23.4225
30.0829-0.149-0.030.1458-0.10740.0429-0.26430.0527-0.0115-0.50940.08220.3095-0.1743-0.0011-0.16520.49230.0034-0.8521-0.10340.701-0.514823.1985-14.5501-42.0669
40.2233-0.0130.03390.1681-0.01110.0478-0.3356-0.21540.2229-0.27110.12020.194-0.1369-0.1039-0.1056-0.0146-0.1527-0.5903-0.1618-0.15030.52618.8533-18.5411-15.121
50.01980.03340.1080.2290.11660.15220.1665-0.52980.01950.3884-0.30390.22850.06680.1123-01.03810.42260.07041.48320.14111.564921.681-39.29549.9471
60.09610.07990.09070.08160.05910.1947-0.41880.4969-0.1756-0.35930.1501-0.6821-0.43670.6374-0.00562.26140.25320.20541.3784-0.04551.405939.713-40.5532-57.2493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 268
2X-RAY DIFFRACTION2chain BB4 - 268
3X-RAY DIFFRACTION3chain CC4 - 268
4X-RAY DIFFRACTION4chain DD4 - 268
5X-RAY DIFFRACTION5chain PP1 - 74
6X-RAY DIFFRACTION6chain QQ1 - 73

+
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://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