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- PDB-3aqm: Structure of bacterial protein (form II) -

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Basic information

Entry
Database: PDB / ID: 3aqm
TitleStructure of bacterial protein (form II)
ComponentsPoly(A) polymerasePolynucleotide adenylyltransferase
KeywordsTRANSFERASE / TRANSFERASE/RNA / ATP-BINDING / NUCLEOTIDE-BINDING / RNA-BINDING / NUCLEOTIDYLTRANSFERASE / ATP Binding / A-Phosphorylation
Function / homologycca-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 / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Poly(A) polymerase
B: Poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1174
Polymers96,0682
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-12 kcal/mol
Surface area37690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.252, 133.252, 176.660
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 / Polynucleotide adenylyltransferase


Mass: 48034.160 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-431
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): K-12
References: UniProt: C9QS13, polynucleotide adenylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-Cl, pH 8.0, 1.2 M 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: Oct 3, 2010
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: 28023 / % possible obs: 99.5 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 14.5
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.1 / Num. unique all: 28023 / % possible all: 99.7

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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 / Resolution: 3.15→29.8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 8691641.76 / 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
Rfree0.287 1388 5 %RANDOM
Rwork0.27 ---
obs0.27 27849 99.3 %-
all-28023 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.2056 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 105.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.99 Å20 Å20 Å2
2--10.99 Å20 Å2
3----21.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.57 Å
Luzzati d res low-5 Å
Luzzati sigma a1.35 Å1.44 Å
Refinement stepCycle: LAST / Resolution: 3.15→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 2 0 6332
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.422
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it4.182.5
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.498 196 4.4 %
Rwork0.481 4252 -
obs--96.7 %
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

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