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- PDB-3aqn: Complex structure of bacterial protein (apo form II) -

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Basic information

Entry
Database: PDB / ID: 3aqn
TitleComplex structure of bacterial protein (apo form II)
ComponentsPoly(A) polymerase
KeywordsTRANSFERASE / TRANSFERASE/RNA / ATP-BINDING / NUCLEOTIDE-BINDING / RNA-BINDING / NUCLEOTIDYLTRANSFERASE / ATP Binding / A-Phosphorylation
Function / homology
Function and homology information


cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsToh, Y. / Takeshita, D. / Tomita , K.
CitationJournal: Structure / Year: 2011
Title: Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases
Authors: Toh, Y. / Takeshita, D. / Nagaike, T. / Numata, T. / Tomita, K.
History
DepositionNov 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Poly(A) polymerase
B: Poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0936
Polymers96,0302
Non-polymers1,0634
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.400, 132.400, 176.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Poly(A) polymerase


Mass: 48015.113 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-431 / Mutation: R234H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: EcDH1_3459 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): K12
References: UniProt: C9QS13, polynucleotide adenylyltransferase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-Cl, pH 8.0, 1.2M sodium acetate, 5mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 22, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 28475 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rsym value: 0.089 / Net I/σ(I): 13.5
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 28475 / Rsym value: 0.462 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AQK

3aqk


Resolution: 3.3→29.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 7931703.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1188 5 %RANDOM
Rwork0.251 ---
obs0.251 23983 99.1 %-
all-28475 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1733 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 128.3 Å2
Baniso -1Baniso -2Baniso -3
1-19.97 Å20 Å20 Å2
2--19.97 Å20 Å2
3----39.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a1.29 Å1.42 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 64 6 6398
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.861.5
X-RAY DIFFRACTIONc_mcangle_it11.922
X-RAY DIFFRACTIONc_scbond_it8.372
X-RAY DIFFRACTIONc_scangle_it13.442.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.478 178 4.6 %
Rwork0.469 3679 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6atp2.paramatp2.top

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