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- PDB-4wbz: tRNA-processing enzyme (apo form 2) -

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Basic information

Entry
Database: PDB / ID: 4wbz
TitletRNA-processing enzyme (apo form 2)
ComponentsPoly A polymerase
KeywordsTRANSFERASE / RNA Nucleotidyltransferase / CCA-adding enzyme / A-adding enzyme
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
A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYamashita, S. / Tomtia, 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 1.2Oct 11, 2017Group: 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_struct_assembly / pdbx_struct_oper_list / reflns_shell
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_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
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: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)93,1012
Polymers93,1012
Non-polymers00
Water00
1
A: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)46,5511
Polymers46,5511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)46,5511
Polymers46,5511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.600, 109.660, 85.270
Angle α, β, γ (deg.)90.000, 110.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46550.711 Da / Num. of mol.: 2 / 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

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEGMME550, NaCl, 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 315 / Detector: CCD / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.51
ReflectionResolution: 3.3→50 Å / Num. obs: 15192 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge F obs: 0.993 / Rmerge(I) obs: 0.17 / Rrim(I) all: 0.195 / Χ2: 0.934 / Net I/σ(I): 9.27 / Num. measured all: 64039
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
3.3-3.390.4491.5581.074293112610361.7992
3.39-3.480.5621.191.444635108910851.36699.6
3.48-3.580.7350.8422.034559107410690.96799.5
3.58-3.690.7370.7522.344475104610460.863100
3.69-3.810.8450.4783.6141929859820.54999.7
3.81-3.940.9060.4334.0742179889860.49799.8
3.94-4.090.8960.3974.7640509509500.457100
4.09-4.260.9210.326.0438439109020.36899.1
4.26-4.450.9170.2347.9336678708670.27199.7
4.45-4.670.9630.1789.834238088070.20599.9
4.67-4.920.9770.14111.7535128298260.16299.6
4.92-5.220.980.1411.4131837467460.161100
5.22-5.580.9790.1411.0529476956960.161100
5.58-6.030.9790.1411.1128226736650.16198.8
6.03-6.60.9850.11413.0325436106080.13199.7
6.6-7.380.9950.07618.0422955485460.08799.6
7.38-8.520.9980.04227.7319834894880.04899.8
8.52-10.440.9990.02838.5316624054050.033100
10.44-14.760.9980.02445.4112253333240.02897.3
14.760.9980.02640.075131791580.03288.3

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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: 4WBY

4wby


Resolution: 3.3→19.867 Å / FOM work R set: 0.8344 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2288 758 5.01 %
Rwork0.2025 14364 -
obs0.2036 15135 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 383.72 Å2 / Biso mean: 145.23 Å2 / Biso min: 61.71 Å2
Refinement stepCycle: final / Resolution: 3.3→19.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 0 0 5937
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026038
X-RAY DIFFRACTIONf_angle_d0.6118091
X-RAY DIFFRACTIONf_chiral_restr0.023901
X-RAY DIFFRACTIONf_plane_restr0.0031005
X-RAY DIFFRACTIONf_dihedral_angle_d11.382367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3078-3.56180.30151520.294628703022
3.5618-3.91770.29021490.253828472996
3.9177-4.47880.25561520.213628723024
4.4788-5.62110.21581500.183428623012
5.6211-19.73460.18721540.168329133067
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)
14.2063-0.63691.96781.3484-0.69332.2504-0.5423-0.77810.52360.6413-0.08490.1654-0.9054-0.20010.60551.0705-0.0024-0.00150.9028-0.07170.92068.964825.0562-59.3919
21.10180.7618-0.23090.6852-0.23621.7606-0.40090.2635-0.4649-0.467-0.0432-0.05760.5267-0.0597-0.09381.4069-0.03380.34331.29620.01360.30488.607823.4836-19.004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:382)A1 - 382
2X-RAY DIFFRACTION2(chain B and resid 1:382)B1 - 382

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