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- PDB-1r89: Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and I... -

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Basic information

Entry
Database: PDB / ID: 1r89
TitleCrystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes
ComponentstRNA nucleotidyltransferase
KeywordsTRANSFERASE / CCA Adding Enzyme / Incoming nucleotide / nucleotidyltransferase superfamily
Function / homology
Function and homology information


tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / Archaeal CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / Archaeal CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXiong, Y. / Li, F. / Wang, J. / Weiner, A.M. / Steitz, T.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes
Authors: Xiong, Y. / Li, F. / Wang, J. / Weiner, A.M. / Steitz, T.A.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6839
Polymers51,4691
Non-polymers1,2148
Water5,945330
1
A: tRNA nucleotidyltransferase
hetero molecules

A: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,36618
Polymers102,9382
Non-polymers2,42816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8920 Å2
ΔGint-120 kcal/mol
Surface area43020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.151, 79.954, 78.145
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

21A-883-

HOH

31A-893-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA nucleotidyltransferase / / tRNA adenylyltransferase / tRNA CCA-pyrophosphorylase / CCA-adding enzyme


Mass: 51469.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: CCA, AF2156 / Production host: Escherichia coli (E. coli) / References: UniProt: O28126, EC: 2.7.7.25

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Non-polymers , 6 types, 338 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Calcium Chloride, Ethanol, Tris, magnesium chloride, sodium chloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein11
2200 mM12CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 48486 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100
Reflection
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.403 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22641 2425 5.1 %RANDOM
Rwork0.18502 ---
obs0.18716 45486 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.18 Å2
2--1.73 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 64 330 4024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213773
X-RAY DIFFRACTIONr_bond_other_d0.0020.023447
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.985082
X-RAY DIFFRACTIONr_angle_other_deg0.78738003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024112
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02840
X-RAY DIFFRACTIONr_nbd_refined0.2080.2739
X-RAY DIFFRACTIONr_nbd_other0.2360.23848
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.180.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.2139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4112.52176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41643513
X-RAY DIFFRACTIONr_scbond_it3.49851597
X-RAY DIFFRACTIONr_scangle_it5.53181569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.899 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.3 330
Rwork0.259 6175
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)
11.7644-0.72820.39682.4309-1.101515.557-0.1682-0.13390.1240.54730.0072-0.2297-1.0912-0.59530.16090.33060.1270.03250.08390.05490.128714.829713.280545.82
21.2378-0.6292-0.0042.0669-0.02382.795-0.113-0.1576-0.10050.18160.1410.1894-0.0675-0.5966-0.0280.11320.15530.00790.28680.07160.208911.060113.593121.1159
32.28942.4539-1.63512.8023-1.61831.54040.0319-0.38770.00370.179-0.0792-0.0842-0.12090.52660.04730.2228-0.0167-0.02660.2564-0.01470.25562.32390.9536-0.2455
41.8626-0.35190.02220.68720.10922.8567-0.3153-0.3752-0.16980.13510.23960.03450.2946-0.11960.07570.26310.11660.03290.1480.04590.219435.7245-7.697317.5387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 12417 - 124
2X-RAY DIFFRACTION1AB - E600 - 6041
3X-RAY DIFFRACTION2AA125 - 258125 - 258
4X-RAY DIFFRACTION2AA1 - 161 - 16
5X-RAY DIFFRACTION3AA338 - 382338 - 382
6X-RAY DIFFRACTION4AA259 - 337259 - 337
7X-RAY DIFFRACTION4AA383 - 437383 - 437
8X-RAY DIFFRACTION4AH - I501 - 5021
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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