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- PDB-3mf1: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -

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Basic information

Entry
Database: PDB / ID: 3mf1
TitleCrystal structure of class II aaRS homologue (Bll0957) complexed with an analogue of glycyl adenylate
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
5'-O-(glycylsulfamoyl)adenosine / Amino acid--[acyl-carrier-protein] ligase 1
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 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
Revision 1.2Jun 19, 2013Group: Atomic model
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,2566
Polymers76,3182
Non-polymers9384
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-38 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.092, 101.304, 50.479
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-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N7O7S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Apr 21, 2009
RadiationMonochromator: Nova optical assembly incorporating graded multilayer optics
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.2→20.82 Å / Num. all: 34009 / Num. obs: 33974 / % possible obs: 99.62 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.04 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.7372
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.08 % / Rmerge(I) obs: 0.55 / Num. measured all: 48773 / Num. unique all: 4839 / % possible all: 99.39

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
TNTrefinement
PDB_EXTRACT3.1data extraction
CrysalisProProdata collection
CrysalisProProdata reduction
REFMAC5.2phasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→20.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1696 4.99 %RANDOM
Rwork0.188 ---
all0.19 33974 --
obs0.19 33974 --
Displacement parametersBiso max: 104.67 Å2 / Biso mean: 27.438 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.216 Å20 Å20 Å2
2---5.163 Å20 Å2
3---2.947 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: LAST / Resolution: 2.2→20.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 56 289 4793
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_dihedral_angle_d1.02
LS refinement shellResolution: 2.2→2.27 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.26 142 4.94 %
Rwork0.22 2733 -
all0.222 2875 -

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