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- PDB-1miy: Crystal structure of Bacillus stearothermophilus CCA-adding enzym... -

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Basic information

Entry
Database: PDB / ID: 1miy
TitleCrystal structure of Bacillus stearothermophilus CCA-adding enzyme in complex with CTP
ComponentstRNA CCA-adding enzyme
KeywordsTRANSLATION / TRANSFERASE / CCA-adding enzyme / tRNA nucleotidyltransferase
Function / homology
Function and homology information


CCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #560 / CCA-adding enzyme, firmicutes / Hydrophobic Seed Protein - #30 / Serum Albumin; Chain A, Domain 1 - #80 / CCA-adding enzyme, C-terminal / tRNA nucleotidyltransferase domain 2 putative / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #560 / CCA-adding enzyme, firmicutes / Hydrophobic Seed Protein - #30 / Serum Albumin; Chain A, Domain 1 - #80 / CCA-adding enzyme, C-terminal / tRNA nucleotidyltransferase domain 2 putative / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Hydrophobic Seed Protein / Serum Albumin; Chain A, Domain 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / CCA-adding enzyme
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsLi, F. / Xiong, Y. / Wang, J. / Cho, H.D. / Weiner, A.M. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP
Authors: Li, F. / Xiong, Y. / Wang, J. / Cho, H.D. / Tomita, K. / Weiner, A.M. / Steitz, T.A.
History
DepositionAug 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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.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_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 CCA-adding enzyme
B: tRNA CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9308
Polymers90,8672
Non-polymers1,0646
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.552, 105.552, 182.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 1 - 404 / Label seq-ID: 1 - 404

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein tRNA CCA-adding enzyme


Mass: 45433.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIB1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5 / Details: NaCl, Tris, MgCl2, pH 7.5, MICRODIALYSIS at 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein11
250 mMTris12pH7.5
3200 mM12NaCl
410 mM12MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 15352 / Observed criterion σ(I): -2 / Redundancy: 10.14 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 32.6
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.8 % / Num. measured all: 155697
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.1.17refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→81.65 Å / Cor.coef. Fo:Fc: 0.813 / Cor.coef. Fo:Fc free: 0.755 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.33125 1518 10.1 %RANDOM
Rwork0.28644 ---
all0.29104 ---
obs0.29104 13534 99.53 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.579 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å2-1.36 Å20 Å2
2---2.72 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 3.52→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 62 34 6320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9688704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.23363
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 3160 / Type: tight positional / Rms dev position: 0.05 Å / Weight position: 0.05
LS refinement shellResolution: 3.52→3.712 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.368 213
Rwork0.32 1902
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)
14.48363.7951.48323.60530.59349.5011-0.5184-0.31180.78560.08250.3083-0.5423-0.5322-0.1430.21010.804-0.2887-0.02481.03830.09020.50742.442722.943640.764
28.40163.0204-2.7791.9748-0.98253.3988-0.66370.73410.6337-0.620.6520.1549-0.729-0.44580.01181.1507-0.4958-0.11690.45170.28370.528415.723338.3417.3141
315.12317.33461.178112.81795.857812.35940.28950.62260.2114-0.1309-0.48760.28710.36590.13750.1980.9327-0.5340.2010.54340.09690.464755.00951.864215.3979
44.8146-0.44210.84063.2549-0.616612.0281-0.33490.03020.4513-0.31030.1461-0.4259-1.12820.37180.18880.7891-0.35970.02021.18090.11481.113931.333238.577850.3621
54.99852.8163-1.89765.9947-1.23783.02960.2197-0.5760.46010.1279-0.38680.2246-1.3043-0.21110.16710.61770.4194-0.12451.1614-0.05080.561811.835734.780574.2041
613.22836.61232.69787.14732.39326.8968-0.09260.12970.86271.0816-0.10090.3926-0.847-0.68990.19350.25290.29560.02011.4390.20880.9456-19.78157.856376.4483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION1A5501 - 5611
3X-RAY DIFFRACTION1B5614
4X-RAY DIFFRACTION2A147 - 340
5X-RAY DIFFRACTION2A5801 - 5807
6X-RAY DIFFRACTION3A341 - 404
7X-RAY DIFFRACTION3A5901 - 5902
8X-RAY DIFFRACTION4B1 - 146
9X-RAY DIFFRACTION4A6614
10X-RAY DIFFRACTION4B6501 - 6611
11X-RAY DIFFRACTION5B147 - 340
12X-RAY DIFFRACTION5B6801 - 6807
13X-RAY DIFFRACTION6B341 - 404
14X-RAY DIFFRACTION6B6901 - 6902
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.32

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