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- PDB-4wc3: Structure of tRNA-processing enzyme complex 1 -

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Basic information

Entry
Database: PDB / ID: 4wc3
TitleStructure of tRNA-processing enzyme complex 1
Components
  • Poly A polymerase
  • RNA 76-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
: / RNA / RNA (> 10) / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 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_assembly / pdbx_struct_assembly_prop / 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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 76-mer


Theoretical massNumber of molelcules
Total (without water)71,0352
Polymers71,0352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-8 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.660, 110.300, 126.250
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) / Strain (production host): BL21(DE3) / References: UniProt: O66728
#2: RNA chain RNA 76-mer


Mass: 24484.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tRNAphe from Thermotoga maritima / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205

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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: 2.87 Å3/Da / Density % sol: 57.22 %
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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 15234 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 110.22 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.129 / Χ2: 0.995 / Net I/σ(I): 17.33 / Num. measured all: 215413
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
3.1-3.180.4063.1231.0714903109810683.24397.3
3.18-3.270.6621.7816052110510912.07298.7
3.27-3.360.8221.3782.5115464106110491.42798.9
3.36-3.470.8491.0633.3115218104710361.10198.9
3.47-3.580.9580.7135.04144809949840.73899
3.58-3.70.9550.5856.28141749729630.60699.1
3.7-3.840.9840.4148.49137429429360.42999.4
3.84-40.990.29611.27131619079000.30799.2
4-4.180.9960.20514.61128028848770.21299.2
4.18-4.380.9960.15318.91118598268220.15899.5
4.38-4.620.9980.11423.87113818098000.11898.9
4.62-4.90.9980.09128.78105297587550.09599.6
4.9-5.240.9990.08130.3898967187140.08499.4
5.24-5.660.9980.08630.1290076616580.0999.5
5.66-6.20.9980.0832.2682666226180.08399.4
6.2-6.930.9980.06538.1475245705680.06899.6
6.93-80.9990.04845.8763165035000.05199.4
8-9.810.03654.8953684454420.03899.3
9.8-13.860.9990.03459.3340443483340.03596
13.860.9990.03854.8412272141190.03955.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementResolution: 3.1→19.841 Å / FOM work R set: 0.7161 / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 762 5.01 %
Rwork0.2406 14456 -
obs0.2429 15218 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 564.52 Å2 / Biso mean: 245.41 Å2 / Biso min: 61.7 Å2
Refinement stepCycle: final / Resolution: 3.1→19.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1623 0 0 4669
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034910
X-RAY DIFFRACTIONf_angle_d0.6216976
X-RAY DIFFRACTIONf_chiral_restr0.025842
X-RAY DIFFRACTIONf_plane_restr0.003593
X-RAY DIFFRACTIONf_dihedral_angle_d14.9362126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1002-3.33860.36061470.33872800294798
3.3386-3.67260.35951520.28462869302199
3.6726-4.19970.2941510.24082870302199
4.1997-5.27460.25391520.23232895304799
5.2746-19.8410.28341600.22283022318299
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)
15.5421-2.5657-0.06683.72253.78333.7136-0.76940.0694-1.28753.1834-0.6162-0.53521.3905-0.4762-0.25561.6061-0.270.58180.6371-0.06491.32264.83138.046147.1573
22.9784-0.5248-0.40960.20120.01580.3656-1.5172-0.8689-0.87412.6652-0.36410.297-0.1560.03221.35166.6699-0.07730.34322.00320.05252.228567.1296157.3428177.2386
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 1:76)B1 - 76

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