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- PDB-3mf2: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -

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Basic information

Entry
Database: PDB / ID: 3mf2
TitleCrystal structure of class II aaRS homologue (Bll0957) complexed with AMP
ComponentsBll0957 protein
KeywordsLIGASE / aminoacyl-tRNA synthetase / seryl-tRNA synthetase / zinc ion / amino acid:[carrier protein] ligase / Bll0957
Function / homology
Function and homology information


: / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding / metal ion binding
Similarity search - Function
Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Amino acid--[acyl-carrier-protein] ligase 1
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsWeygand-Durasevic, I. / Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
Authors: Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. / Weygand-Durasevic, I.
#1: Journal: Embo J. / Year: 2006
Title: Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition
Authors: Bilokapic, S. / Maier, T. / Ahel, D. / Gruic-Sovulj, I. / Soll, D. / Weygand-Durasevic, I. / Ban, N.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bll0957 protein
B: Bll0957 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3288
Polymers76,3182
Non-polymers1,0096
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-43 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.670, 100.240, 50.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bll0957 protein / class II aaRS homologue


Mass: 38159.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA110 / Gene: bll0957 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89VT8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 4.6
Details: PEG 4000, gycerol, pH 4.6, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2008
RadiationMonochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionNumber: 278833 / Rmerge(I) obs: 0.055 / D res high: 2.15 Å / D res low: 46.74 Å / Num. obs: 35847 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.3946.74256999.310.022
4.546.39461199.910.031
3.714.54598999.810.031
3.223.71706899.910.042
2.883.22798510010.068
2.632.88885299.910.112
2.432.63962610010.188
2.282.431032710010.263
2.152.281063896.810.407
ReflectionResolution: 2.15→46.74 Å / Num. all: 35915 / Num. obs: 35847 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.182 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.23
Reflection shellResolution: 2.15→2.28 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 40479 / Num. unique obs: 10638 / % possible all: 96.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
SHARPphasing
TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.15→29.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1793 5 %RANDOM
Rwork0.176 ---
all0.178 35847 --
obs0.178 35847 --
Displacement parametersBiso max: 135.85 Å2 / Biso mean: 41.383 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.082 Å20 Å20 Å2
2---3.564 Å20 Å2
3---1.482 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 60 170 4876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.01
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.248 144 5.02 %
Rwork0.191 2727 -
all0.194 2871 -

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