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- PDB-4wc7: Structure of tRNA-processing enzyme complex 5 -

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Basic information

Entry
Database: PDB / ID: 4wc7
TitleStructure of tRNA-processing enzyme complex 5
Components
  • Poly A polymerase
  • RNA (75-MER)
KeywordsTRANSFERASE/RNA / RNA Nucleotidyltransferase / CCA-adding enzyme / A-adding enzyme / TRANSFERASE-RNA complex
Function / homology
Function and homology information


ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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
CYTIDINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Agency (JST)LS135 Japan
CitationJournal: Structure / Year: 2015
Title: Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Authors: Yamashita, S. / Martinez, A. / Tomita, K.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly A polymerase
B: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1893
Polymers70,7062
Non-polymers4831
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-6 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.870, 111.390, 127.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly A polymerase / A-adding enzyme


Mass: 46550.711 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 443-824
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: pcnB1, aq_411 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: O66728
#2: RNA chain RNA (75-MER)


Mass: 24155.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tRNAphe from Thermotoga maritima / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: isopropanol, potassium chloride, magnesium chloride, sodium cacodylate

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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: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 15717 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 91.18 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.149 / Χ2: 0.977 / Net I/σ(I): 11.61 / Num. measured all: 101099
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.180.6441.591.237187112111041.72798.5
3.18-3.270.7261.1891.757569114711471.291100
3.27-3.370.8750.8422.517043106610660.914100
3.37-3.470.8970.72.917103107610760.76100
3.47-3.580.9430.4724.276658101110110.513100
3.58-3.710.9790.3745.336673101910180.40799.9
3.71-3.850.9780.3076.3961909419410.333100
3.85-4.010.9860.228.3861169339330.239100
4.01-4.180.9950.1510.9158748948940.163100
4.18-4.390.9940.13112.856078628620.142100
4.39-4.620.9950.10315.9452658148140.112100
4.62-4.910.9970.08418.250457867860.091100
4.91-5.240.9970.08218.7246597287280.089100
5.24-5.660.9970.08917.5843166786780.097100
5.66-6.20.9970.08319.1640436406390.09199.8
6.2-6.940.9960.0722.7836555825820.076100
6.94-8.010.9980.04729.8131475215200.05299.8
8.01-9.810.9990.03637.1725724484480.04100
9.81-13.870.9980.03439.9617893563450.03896.9
13.870.9970.03537.795882211250.03956.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WC2

4wc2


Resolution: 3.102→19.835 Å / FOM work R set: 0.635 / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3218 786 5.01 %
Rwork0.2772 14912 -
obs0.2794 15698 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 553.62 Å2 / Biso mean: 223.21 Å2 / Biso min: 65.28 Å2
Refinement stepCycle: final / Resolution: 3.102→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1601 29 0 4676
Biso mean--174.36 --
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034915
X-RAY DIFFRACTIONf_angle_d0.586984
X-RAY DIFFRACTIONf_chiral_restr0.022841
X-RAY DIFFRACTIONf_plane_restr0.003594
X-RAY DIFFRACTIONf_dihedral_angle_d14.7072128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1024-3.2960.39311270.38132406253399
3.296-3.54910.39151290.32824442573100
3.5491-3.90380.3641300.309224662596100
3.9038-4.46310.3291310.273424862617100
4.4631-5.6020.31021320.265525062638100
5.602-19.83570.2821370.24582604274199
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)
12.0486-0.5854-0.0513.68651.30460.4733-0.2598-0.2313-0.70892.1537-0.3828-0.08630.5219-0.13370.45820.8909-0.26050.3490.56170.18522.1165.1765139.5082148.4146
24.3561-0.5306-2.13080.23920.50341.3642-1.5657-0.9737-1.16451.61030.2940.40980.16570.36971.22335.08140.230.00961.70620.09422.279566.8514159.1287179.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:381)A1 - 381
2X-RAY DIFFRACTION2(chain B and resid 1:75)B1 - 75

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