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- PDB-5hc9: Thermotoga maritima CCA-adding enzyme complexed with tRNA_CCA -

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Basic information

Entry
Database: PDB / ID: 5hc9
TitleThermotoga maritima CCA-adding enzyme complexed with tRNA_CCA
Components
  • tRNA nucleotidyl transferase-related protein
  • tRNAphe
KeywordsTRANSFERASE / tRNA / CCA-adding enzyme
Function / homology
Function and homology information


RNA 3'-end processing / nucleotidyltransferase activity / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain ...cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA nucleotidyl transferase-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Agency (JST)LS135 Japan
CitationJournal: Structure / Year: 2016
Title: Mechanism of 3'-Matured tRNA Discrimination from 3'-Immature tRNA by Class-II CCA-Adding Enzyme
Authors: Yamashita, S. / Tomita, K.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Oct 11, 2017Group: Data collection / Category: diffrn_source / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_site / _reflns_shell.percent_possible_all
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: tRNA nucleotidyl transferase-related protein
B: tRNA nucleotidyl transferase-related protein
C: tRNAphe
D: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0796
Polymers152,0304
Non-polymers492
Water0
1
A: tRNA nucleotidyl transferase-related protein
C: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0393
Polymers76,0152
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-30 kcal/mol
Surface area32140 Å2
MethodPISA
2
B: tRNA nucleotidyl transferase-related protein
D: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0393
Polymers76,0152
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-31 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.180, 96.190, 108.580
Angle α, β, γ (deg.)90.000, 110.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA nucleotidyl transferase-related protein / tRNA nucleotidyltransferase


Mass: 51530.617 Da / Num. of mol.: 2 / Fragment: UNP residues 437-863
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0715, Tmari_0715 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZH4, CCA tRNA nucleotidyltransferase
#2: RNA chain tRNAphe


Mass: 24484.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, magnesium chloride, Tris-Cl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 42228 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 69.42 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.217 / Χ2: 0.951 / Net I/σ(I): 10.26 / Num. measured all: 322538
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.9-37.40.552.2731.122009310830352.58898.3
2.97-3.050.6841.8661.3323494305530432.00199.6
3.05-3.140.7991.4361.8222699294629401.53999.8
3.14-3.240.8611.0952.322036285428501.17399.9
3.24-3.350.9150.8382.9421465278227780.89999.9
3.35-3.460.9360.6693.6820912271227060.71799.8
3.46-3.590.960.5024.8720077260826040.53899.8
3.59-3.740.9760.3556.4419254249824960.38199.9
3.74-3.910.9830.2927.7418631241824120.31499.8
3.91-4.10.9910.20510.1617578228722800.2299.7
4.1-4.320.9930.15712.8816882218821860.16899.9
4.32-4.580.9960.11816.2215997208220790.12799.9
4.58-4.90.9960.10617.8114885194219430.114100
4.9-5.290.9960.10418.1813955182918210.11199.6
5.29-5.790.9960.10418.2612851167916810.112100
5.79-6.480.9960.09819.1611566151615130.10599.8
6.48-7.480.9970.07424.1110164135013460.0899.7
7.48-9.160.9990.04336.158559115611490.04799.4
9.16-12.960.9990.03545.3464288888860.03799.8
12.960.9980.03646.2530965144800.03993.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H38

3h38


Resolution: 2.9→20 Å / FOM work R set: 0.7369 / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 2102 5 %Random selection
Rwork0.2146 39922 --
obs0.2171 42024 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 383.51 Å2 / Biso mean: 132.24 Å2 / Biso min: 37.09 Å2
Refinement stepCycle: final / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 3246 2 0 10128
Biso mean--67.13 --
Num. residues----987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210633
X-RAY DIFFRACTIONf_angle_d0.63815070
X-RAY DIFFRACTIONf_chiral_restr0.0241806
X-RAY DIFFRACTIONf_plane_restr0.0041352
X-RAY DIFFRACTIONf_dihedral_angle_d14.2684538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8971-2.96430.46551370.39752583272097
2.9643-3.03820.40591390.363926422781100
3.0382-3.120.3671390.32942637277699
3.12-3.21150.34481400.301526522792100
3.2115-3.31470.33861390.29152646278599
3.3147-3.43260.31511390.26342644278399
3.4326-3.56920.33061390.252726432782100
3.5692-3.73070.25921410.222626712812100
3.7307-3.9260.24861400.208826772817100
3.926-4.16980.23661400.192626532793100
4.1698-4.48840.24111410.17526702811100
4.4884-4.93390.19041420.171526942836100
4.9339-5.63370.24181410.19126792820100
5.6337-7.04540.29881410.222226852826100
7.0454-19.93840.20611440.159327462890100
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)
12.0680.19781.70420.74930.34272.08970.03620.3609-0.0433-0.05150.0252-0.0866-0.01230.5505-0.04480.5605-0.0057-0.00070.5372-0.00180.38853.600811.0411223.4388
20.8798-0.09680.84910.4875-0.10823.58280.07460.3398-0.1806-0.02630.0358-0.10320.25030.2724-0.08080.48370.0189-0.07160.4655-0.0970.560330.619311.1744267.0952
32.17370.2799-0.70241.361-0.61910.96220.17210.4463-0.7196-0.7102-0.3005-0.88920.29361.04710.1631.48340.20160.09872.2594-0.16421.534431.659-3.6515214.4598
41.5258-0.1393-0.04131.65110.77831.5395-0.08990.73511.0129-1.00310.3349-0.3488-1.08160.7598-0.10531.392-0.43250.07031.33250.21661.26838.344341.5012255.7985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:425)A1 - 425
2X-RAY DIFFRACTION2(chain B and resid 1:425)B1 - 425
3X-RAY DIFFRACTION3(chain C and resid 1:76)C1 - 76
4X-RAY DIFFRACTION4(chain D and resid 1:76)D1 - 76

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