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- PDB-1miv: Crystal structure of Bacillus stearothermophilus CCA-adding enzyme -

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Basic information

Entry
Database: PDB / ID: 1miv
TitleCrystal structure of Bacillus stearothermophilus CCA-adding enzyme
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
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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)91,8534
Polymers91,8042
Non-polymers492
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.861, 105.861, 183.658
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 B
21A B

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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 61.97 %
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: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 15392 / % possible obs: 99.46 % / Observed criterion σ(I): -2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / % possible obs: 99.4 % / Num. measured all: 124736
Reflection shell
*PLUS
% possible obs: 99.4 % / 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: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.818 / Cor.coef. Fo:Fc free: 0.78 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32779 1547 10.1 %RANDOM
Rwork0.28862 ---
all0.29256 ---
obs0.29256 13845 99.46 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.988 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-1.22 Å20 Å2
2---2.43 Å20 Å2
3---3.65 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 2 36 6264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9578612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2820.23153
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.21
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: 3132 / Type: tight positional / Rms dev position: 0.05 Å / Weight position: 0.05
LS refinement shellResolution: 3.5→3.683 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.361 206
Rwork0.344 1950
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)
15.50362.68071.06463.8402-1.983615.5503-0.2881-0.49260.76910.09060.4346-0.14980.1449-0.5445-0.14650.6682-0.2259-0.13050.99520.16430.87072.625222.578441.348
210.96183.7062-2.46541.926-1.8563.7073-0.2720.43040.9395-0.55050.69250.5226-0.9729-0.8059-0.42061.2284-0.3996-0.08990.65720.45440.712315.691138.547717.465
315.80299.29261.586624.3686.22758.5117-0.08990.62680.5706-1.20260.16690.18841.0380.5957-0.07690.9504-0.56640.12810.61930.18290.40255.073152.207515.4254
44.1568-1.03350.41657.60220.81713.21760.05090.2910.2737-0.4597-0.2537-0.5613-1.36420.51830.20280.8148-0.2292-0.08791.32470.25011.094131.613838.406650.4762
54.84392.1331-2.59435.0914-2.09014.9143-0.02850.15520.7166-0.08940.06490.2719-1.479-0.3935-0.03640.79690.5062-0.28891.0174-0.06780.58711.86234.813174.8208
620.66394.50123.72049.2157-0.15368.3933-0.24340.26220.91680.61530.35720.3013-0.2861-0.5533-0.11390.19830.3388-0.07471.3631-0.24120.8509-19.90527.825377.0798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1461 - 146
3X-RAY DIFFRACTION2AA147 - 340147 - 340
5X-RAY DIFFRACTION3AA341 - 404341 - 404
7X-RAY DIFFRACTION4BB1 - 1461 - 146
9X-RAY DIFFRACTION5BB147 - 340147 - 340
11X-RAY DIFFRACTION6BB341 - 404341 - 404
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.327 / Rfactor Rwork: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS

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