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

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Basic information

Entry
Database: PDB / ID: 3wbz
TitleCrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with ATP
ComponentsLikely histidyl tRNA-specific guanylyltransferase
KeywordsTRANSFERASE
Function / homologytRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 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 1.2Feb 5, 2014Group: Other
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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: Likely histidyl tRNA-specific guanylyltransferase
B: Likely histidyl tRNA-specific guanylyltransferase
C: Likely histidyl tRNA-specific guanylyltransferase
D: Likely histidyl tRNA-specific guanylyltransferase
E: Likely histidyl tRNA-specific guanylyltransferase
F: Likely histidyl tRNA-specific guanylyltransferase
G: Likely histidyl tRNA-specific guanylyltransferase
H: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,21248
Polymers261,5148
Non-polymers8,69840
Water6,575365
1
A: Likely histidyl tRNA-specific guanylyltransferase
B: Likely histidyl tRNA-specific guanylyltransferase
C: Likely histidyl tRNA-specific guanylyltransferase
D: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,10624
Polymers130,7574
Non-polymers4,34920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18420 Å2
ΔGint-169 kcal/mol
Surface area45830 Å2
MethodPISA
2
E: Likely histidyl tRNA-specific guanylyltransferase
F: Likely histidyl tRNA-specific guanylyltransferase
G: Likely histidyl tRNA-specific guanylyltransferase
H: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,10624
Polymers130,7574
Non-polymers4,34920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18420 Å2
ΔGint-170 kcal/mol
Surface area46580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.830, 217.870, 87.240
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Likely histidyl tRNA-specific guanylyltransferase


Mass: 32689.248 Da / Num. of mol.: 8
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, tRNAHis guanylyltransferase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Bis-Tris propan, NaNO3, PEG3350, pH 8.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→44.008 Å / Num. obs: 97820 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.468 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.93
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
2.39-2.540.3480.2595.195144016208145470.30689.8
2.54-2.710.210.17885891515256151910.20699.6
2.71-2.930.1260.10912.335474614152140820.12799.5
2.93-3.210.0690.06519.35033113083129940.07599.3
3.21-3.580.0350.03730.224518911856117640.04399.2
3.58-4.130.0220.02641.243947410453103700.0399.2
4.13-5.050.0170.02348.5733111884387810.02799.3
5.05-7.090.0170.02349.425737689168440.02799.3
7.090.0120.01852.811542394832460.02182.2

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Processing

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

3ote


Resolution: 2.392→42.259 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8504 / SU ML: 0.26 / Phase error: 22.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 3528 3.61 %RANDOM
Rwork0.1762 ---
obs0.1773 97819 97.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.1 Å2 / Biso mean: 49.2137 Å2 / Biso min: 15.61 Å2
Refinement stepCycle: LAST / Resolution: 2.392→42.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17474 0 520 365 18359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918513
X-RAY DIFFRACTIONf_angle_d1.26125081
X-RAY DIFFRACTIONf_chiral_restr0.0532527
X-RAY DIFFRACTIONf_plane_restr0.0063080
X-RAY DIFFRACTIONf_dihedral_angle_d17.7356971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.392-2.42480.2371160.22752715283170
2.4248-2.45940.26571200.21673508362893
2.4594-2.49620.26391680.21713844401298
2.4962-2.53520.27791270.216637993926100
2.5352-2.57670.27131490.227338794028100
2.5767-2.62110.28411480.221138433991100
2.6211-2.66880.2691630.202838323995100
2.6688-2.72010.27341510.213238433994100
2.7201-2.77560.25231450.204238774022100
2.7756-2.8360.26911250.199538243949100
2.836-2.90190.22961310.203439014032100
2.9019-2.97450.2531560.20623846400299
2.9745-3.05490.25171460.2083799394599
3.0549-3.14470.28351510.215338534004100
3.1447-3.24620.21661540.20143879403399
3.2462-3.36220.24981340.19493825395999
3.3622-3.49670.17611310.17813864399599
3.4967-3.65580.2141360.17423865400199
3.6558-3.84840.17031320.16663846397899
3.8484-4.08940.19151430.1593862400599
4.0894-4.40480.19331560.14813870402699
4.4048-4.84750.16281570.135338373994100
4.8475-5.54760.16931420.149938724014100
5.5476-6.98430.18871300.170838984028100
6.9843-42.26580.17381170.15933301341884
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)
11.85850.4014-0.40890.7352-0.33971.33460.04550.0057-0.03860.11170.01640.1635-0.0557-0.1202-0.0450.15430.02360.02690.2370.01350.3691-9.802519.493528.3513
21.56050.1450.41770.6395-0.07421.12320.11050.0792-0.22390.1317-0.0038-0.10220.0730.1232-0.09790.1795-0.0015-0.06040.2505-0.01730.299620.696921.313132.611
30.8051-0.4124-0.07921.68670.11871.4915-0.1020.11910.0184-0.20650.13610.2776-0.3797-0.0181-0.01950.3375-0.0505-0.07930.29380.0260.35032.743647.1035-5.7224
40.5355-0.416-0.40391.8524-0.03661.7225-0.06050.059-0.0744-0.32230.0637-0.09830.05720.52070.020.2221-0.0051-0.02660.4744-0.06890.307519.13622.3047-12.3471
51.27770.07290.37381.6586-0.27441.05490.02240.0131-0.04850.44090.04190.4376-0.1915-0.1273-0.03460.39560.01930.16310.2426-0.00990.345311.963670.138144.2087
61.82280.48040.4341.4368-0.04190.8627-0.0263-0.05810.0870.486-0.03-0.1909-0.1230.26210.03130.5578-0.077-0.0430.3586-0.01130.281638.437883.51850.2034
71.4578-0.28530.10651.09990.09311.0019-0.11360.12550.2854-0.33020.1040.2731-0.5015-0.11490.00850.75010.0426-0.0520.41990.09930.439912.7067100.815410.7959
81.2931-0.4163-0.16661.2133-0.34171.80270.02290.21730.1214-0.2581-0.0302-0.1823-0.38560.6777-0.00350.5122-0.1590.08340.69010.02850.292738.557586.07665.1593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0
2X-RAY DIFFRACTION2chain BB0
3X-RAY DIFFRACTION3chain CC0
4X-RAY DIFFRACTION4chain DD0
5X-RAY DIFFRACTION5chain EE0
6X-RAY DIFFRACTION6chain FF0
7X-RAY DIFFRACTION7chain GG0
8X-RAY DIFFRACTION8chain HH0

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