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

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Basic information

Entry
Database: PDB / ID: 1miw
TitleCrystal structure of Bacillus stearothermophilus CCA-adding enzyme in complex with ATP
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
ADENOSINE-5'-TRIPHOSPHATE / CCA-adding enzyme
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 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 / Version format compliance

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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)92,9168
Polymers91,8042
Non-polymers1,1126
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.632, 105.632, 184.159
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: 2 / 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: 45902.227 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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 61.91 %
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: 1.1063, 0.9786, 0.9789, 0.9560
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2002
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.10631
20.97861
30.97891
40.9561
ReflectionResolution: 3→81.65 Å / Num. obs: 24280 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 9.95 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 42
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 241651
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.1.17refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→81.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26323 2373 9.8 %RANDOM
Rwork0.22803 ---
all0.2314 ---
obs0.2314 21907 99.91 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 88.308 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.9 Å20 Å2
2--1.79 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 3→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 66 42 6334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.978716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.23010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0881.53932
X-RAY DIFFRACTIONr_mcangle_it2.15126300
X-RAY DIFFRACTIONr_scbond_it2.94532496
X-RAY DIFFRACTIONr_scangle_it5.2244.52416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3167 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
tight thermal0.10.5
LS refinement shellResolution: 3.001→3.163 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.426 317
Rwork0.364 3158
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)
13.61941.68740.87151.7346-0.56145.5456-0.0003-0.4460.33550.0409-0.02470.0967-0.1135-0.11760.02490.4018-0.1694-0.02870.3919-0.11920.18622.449123.107740.8953
25.33552.3197-1.53041.2503-0.39041.0131-0.55050.66750.5285-0.65490.4470.062-0.5499-0.05670.10340.9561-0.2729-0.18570.24440.19540.29715.875638.154617.3937
311.60765.8547-1.341912.1735-0.24696.9182-0.03610.30110.37320.1669-0.07580.35880.5101-0.14340.11190.8199-0.29050.00720.23250.14320.16455.432351.638215.8693
43.21650.0932-0.73133.3139-0.9648.2565-0.12620.14220.5925-0.2690.0949-0.5048-1.01131.2190.03120.5608-0.4978-0.06540.72370.02130.527631.409739.162251.023
53.29082.121-0.95974.1394-0.89132.9144-0.0657-0.85820.5290.2308-0.0190.2922-1.1389-0.23540.08470.53140.185-0.02920.6012-0.38910.313711.963635.186874.7651
617.58863.4782-1.30994.32810.07245.49720.10290.4161.13490.24640.24230.3052-0.1712-0.2971-0.34520.13150.10230.10540.98520.05430.1952-19.7277.939376.4184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1461 - 146
2X-RAY DIFFRACTION1AG55011
3X-RAY DIFFRACTION2AA147 - 340147 - 340
4X-RAY DIFFRACTION2AC - D5601 - 56111
5X-RAY DIFFRACTION3AA341 - 404341 - 404
6X-RAY DIFFRACTION3AI5602 - 66141 - 21
7X-RAY DIFFRACTION4BB1 - 1461 - 146
8X-RAY DIFFRACTION4BH65011
9X-RAY DIFFRACTION5BB147 - 340147 - 340
10X-RAY DIFFRACTION5BE - F6601 - 66111
11X-RAY DIFFRACTION6BB341 - 404341 - 404
12X-RAY DIFFRACTION6BJ5614 - 69021 - 21
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS

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