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- PDB-4wc1: Structure of tRNA-processing enzyme with CTP -

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Basic information

Entry
Database: PDB / ID: 4wc1
TitleStructure of tRNA-processing enzyme with CTP
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 / RNA 3'-end processing / 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain ...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 / 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
CYTIDINE-5'-TRIPHOSPHATE / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (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_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_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: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0684
Polymers93,1012
Non-polymers9662
Water0
1
A: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0342
Polymers46,5511
Non-polymers4831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0342
Polymers46,5511
Non-polymers4831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 108.090, 84.920
Angle α, β, γ (deg.)90.000, 110.080, 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
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEGMME550, sodium chloride, Tris-Cl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.49
ReflectionResolution: 3.1→50 Å / Num. obs: 17858 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.088 / Χ2: 0.938 / Net I/σ(I): 16.08 / Num. measured all: 67902
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.180.5051.2671.194879133913061.47697.5
3.18-3.260.5860.9441.635073132313171.09699.5
3.26-3.360.8220.6182.354742123412320.71899.8
3.36-3.460.9120.4233.454763123812350.49199.8
3.46-3.570.9680.2794.894576118911880.32499.9
3.57-3.70.9740.2295.994530118411760.26799.3
3.7-3.840.9880.158.464277111111070.17599.6
3.84-40.9930.10911.284088106010570.12799.7
4-4.170.9960.07915.133953103410260.09299.2
4.17-4.380.9960.06718.2137889839810.07899.8
4.38-4.620.9980.04924.2235519259220.05799.7
4.62-4.90.9980.03928.734819139060.04599.2
4.9-5.230.9980.03828.6231538248240.045100
5.23-5.650.9980.04128.5129917887830.04799.4
5.65-6.190.9980.03829.926907097090.044100
6.19-6.920.9990.03335.0224596596520.03898.9
6.92-7.990.9990.02445.6321205795770.02899.7
7.99-9.790.9990.02151.8116324994630.02592.8
9.79-13.850.9980.0251.958463732790.02474.8
13.850.9970.02447.583102211180.0353.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementStarting model: 4WBY

4wby


Resolution: 3.1→19.833 Å / FOM work R set: 0.6607 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2309 894 5.02 %
Rwork0.1809 16891 -
obs0.1846 17801 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 438.49 Å2 / Biso mean: 135.59 Å2 / Biso min: 49.63 Å2
Refinement stepCycle: final / Resolution: 3.1→19.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 58 0 5995
Biso mean--85.97 --
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056098
X-RAY DIFFRACTIONf_angle_d0.9258185
X-RAY DIFFRACTIONf_chiral_restr0.035909
X-RAY DIFFRACTIONf_plane_restr0.0041009
X-RAY DIFFRACTIONf_dihedral_angle_d14.7872395
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 (%)
3.1001-3.29330.33091500.2952831298195
3.2933-3.54590.28811490.23352832298195
3.5459-3.89960.24631490.20812833298295
3.8996-4.45670.2441490.17812844299395
4.4567-5.58820.19491490.16462825297495
5.5882-18.27720.21031440.1552726287089
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)
13.0712-1.79870.01482.4067-1.22740.9545-0.4097-0.52930.54980.94190.1326-0.1084-0.73530.05040.23971.1403-0.0195-0.37151.0556-0.09460.60628.490331.4457-58.7401
23.6141.7466-1.76173.0639-0.13481.9433-0.78860.5234-0.7072-1.20830.0181-0.08030.6079-0.15740.65511.19170.01060.10690.91760.01650.50868.623930.1538-18.6749
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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