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- PDB-3wc2: Crystal structure of C. albicans tRNA(His) guanylyltransferase (T... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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

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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: 2.25 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

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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

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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

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