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- PDB-3wc0: Crystal structure of C. albicans tRNA(His) guanylyltransferase (T... -

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Basic information

Entry
Database: PDB / ID: 3wc0
TitleCrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with GTP
ComponentsLikely histidyl tRNA-specific guanylyltransferase
KeywordsTRANSFERASE
Function / homologytRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / GUANOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 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 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
I: Likely histidyl tRNA-specific guanylyltransferase
J: Likely histidyl tRNA-specific guanylyltransferase
K: Likely histidyl tRNA-specific guanylyltransferase
L: Likely histidyl tRNA-specific guanylyltransferase
M: Likely histidyl tRNA-specific guanylyltransferase
N: Likely histidyl tRNA-specific guanylyltransferase
O: Likely histidyl tRNA-specific guanylyltransferase
P: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,93696
Polymers523,02816
Non-polymers17,90880
Water27015
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)135,23424
Polymers130,7574
Non-polymers4,47720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)135,23424
Polymers130,7574
Non-polymers4,47720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Likely histidyl tRNA-specific guanylyltransferase
J: Likely histidyl tRNA-specific guanylyltransferase
K: Likely histidyl tRNA-specific guanylyltransferase
L: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,23424
Polymers130,7574
Non-polymers4,47720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Likely histidyl tRNA-specific guanylyltransferase
N: Likely histidyl tRNA-specific guanylyltransferase
O: Likely histidyl tRNA-specific guanylyltransferase
P: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,23424
Polymers130,7574
Non-polymers4,47720
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Likely histidyl tRNA-specific guanylyltransferase
B: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-22 kcal/mol
Surface area26500 Å2
MethodPISA
6
C: Likely histidyl tRNA-specific guanylyltransferase
D: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-24 kcal/mol
Surface area26520 Å2
MethodPISA
7
E: Likely histidyl tRNA-specific guanylyltransferase
F: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-25 kcal/mol
Surface area23150 Å2
MethodPISA
8
G: Likely histidyl tRNA-specific guanylyltransferase
H: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area26430 Å2
MethodPISA
9
I: Likely histidyl tRNA-specific guanylyltransferase
J: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-23 kcal/mol
Surface area24830 Å2
MethodPISA
10
K: Likely histidyl tRNA-specific guanylyltransferase
L: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-25 kcal/mol
Surface area24440 Å2
MethodPISA
11
M: Likely histidyl tRNA-specific guanylyltransferase
N: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area26450 Å2
MethodPISA
12
O: Likely histidyl tRNA-specific guanylyltransferase
P: Likely histidyl tRNA-specific guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61712
Polymers65,3782
Non-polymers2,23910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.430, 217.560, 140.910
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments: (Selection details: chain 'P' and segid 'P ' RESTRAINED TORSIONS: 21178 Histogram...)

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Components

#1: Protein
Likely histidyl tRNA-specific guanylyltransferase


Mass: 32689.248 Da / Num. of mol.: 16
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: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
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: Jul 6, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.03→44.58 Å / Num. obs: 98555 / % possible obs: 98.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.03→3.03 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.03 / % possible all: 96.5

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WBZ

3wbz


Resolution: 3.03→44.58 Å / SU ML: 0.41 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.2393 7040 7.14 %
Rwork0.1983 --
obs0.2012 98545 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35254 0 1072 15 36341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537292
X-RAY DIFFRACTIONf_angle_d0.99950527
X-RAY DIFFRACTIONf_dihedral_angle_d16.92114097
X-RAY DIFFRACTIONf_chiral_restr0.0435096
X-RAY DIFFRACTIONf_plane_restr0.0046202
Refine LS restraints NCSType: POSITIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.03-3.06350.36882070.3324264286
3.0635-3.09950.32792320.2968306099
3.0995-3.13730.33082420.2876306599
3.1373-3.1770.3122330.2847305199
3.177-3.21880.31342370.2644304899
3.2188-3.26290.3422280.2601305199
3.2629-3.30950.30172090.2694304099
3.3095-3.35890.33932570.2689311099
3.3589-3.41130.31812110.2613304599
3.4113-3.46720.2892240.2403307499
3.4672-3.5270.29072370.2346306199
3.527-3.59110.28492380.2296303999
3.5911-3.66010.26752560.22563057100
3.6601-3.73480.27562270.2178307799
3.7348-3.8160.26092350.2012307099
3.816-3.90470.25192340.2117303899
3.9047-4.00230.25992300.20243092100
4.0023-4.11040.2432300.2047307599
4.1104-4.23130.23322350.19163042100
4.2313-4.36780.2152390.1757308999
4.3678-4.52370.20442260.1673307099
4.5237-4.70460.21732640.17183035100
4.7046-4.91850.19012320.17043061100
4.9185-5.17750.22642190.17913131100
5.1775-5.50130.21492540.1733048100
5.5013-5.92520.22272660.1893031100
5.9252-6.51980.21352210.17393112100
6.5198-7.45940.22152250.17663111100
7.4594-9.38360.18772430.16213096100
9.3836-44.58470.20822490.1738298495
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)
10.14490.0478-0.09630.0307-0.03690.07180.1155-0.04160.19010.1359-0.0492-0.1708-0.03440.21440.10360.6712-0.0168-0.32040.67730.14620.662460.829424.19876.5417
20.00750.0136-0.01280.0481-0.03350.070.07890.02740.01790.0218-0.0814-0.1175-0.00410.07090.10150.4708-0.0726-0.10030.33410.25570.500651.042740.414852.2824
30.0660.0578-0.01890.0731-0.00470.04310.0388-0.1554-0.15780.0938-0.03740.1116-0.0665-0.0264-00.71190.0421-0.00340.57260.16610.449319.467830.61690.3286
40.1292-0.0703-0.11040.05610.06430.09980.01520.0293-0.13690.0465-0.01590.0478-0.1249-0.167-00.49370.0126-0.09220.37510.13330.551713.31819.979362.0362
50.0221-0-0.02740.1991-0.09830.12430.1203-0.3119-0.0461-0.0156-0.1382-0.04860.1169-0.0693-0.07230.4789-0.22920.00040.92190.22240.3289.1494-33.4595-4.0074
60.21420.0250.06980.16960.07470.08650.02-0.3033-0.0757-0.0993-0.07950.2066-0.0425-0.0269-0.00550.3999-0.0174-0.06610.37380.0440.398-0.1705-33.121-33.6161
70.19980.14520.12610.17290.06260.0870.1767-0.2343-0.1026-0.11030.0758-0.2426-0.11490.13390.00990.33390.07570.04370.5207-0.09290.495349.2472-30.5744-25.3128
80.2882-0.00070.03550.03410.02650.1275-0.13720.01990.055-0.2880.2142-0.0462-0.0060.10020.00970.4702-0.10320.01980.2747-0.07530.246735.3994-4.8573-34.657
90.24430.00680.09660.0912-0.01440.24650.17860.09870.17210.1776-0.13220.22710.04550.05960.36970.5612-0.05080.29210.3534-0.08130.347735.5453-28.555964.2467
100.10030.0272-0.03110.21650.05440.05030.02240.17910.15110.0474-0.04610.4173-0.0814-0.07960.00260.37660.0529-0.06670.57220.13050.44129.6702-29.518434.0404
110.11910.18220.05510.2820.07540.02990.17270.2316-0.04690.07060.0531-0.2805-0.02960.11240.00950.38660.11920.02550.4784-0.13770.447377.8541-31.423947.9263
120.1165-0.05770.0740.17890.06790.1263-0.20120.3190.1763-0.20510.1836-0.09480.05210.20220.06170.5986-0.17620.05070.68440.19680.406968.5641-5.523134.5127
130.23520.13140.02060.09080.01320.10530.0035-0.30750.0956-0.04860.04060.07930.07130.06640.00130.29060.03920.05340.4612-0.02660.4491-1.128429.552422.1219
140.2641-0.0316-0.05420.01420.03430.1251-0.05360.2277-0.05660.07640.12750.12670.01230.01890.02090.28-0.0749-0.04420.25350.05530.3896-7.166216.6297-5.2618
150.3086-0.0293-0.12630.10880.06730.28340.0375-0.14710.3541-0.02010.1354-0.09350.03080.1520.0230.3223-0.09730.03430.4867-0.04630.627638.951433.42024.5191
160.0152-0.007-0.01230.01550.03390.0943-0.00630.1970.28280.00910.01840.0220.024-0.04410.14110.3317-0.14590.03590.52190.33750.674223.387247.8846-17.5683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain M
14X-RAY DIFFRACTION14chain N
15X-RAY DIFFRACTION15chain O
16X-RAY DIFFRACTION16chain P

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