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

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Basic information

Entry
Database: PDB / ID: 3pzc
TitleCrystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A
ComponentsAmino acid--[acyl-carrier-protein] ligase 1
KeywordsLIGASE / amino acid:[carrier protein] ligase / seryl-tRNA synthetase / carrier protein / Coenzyme A
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
ACETATE ION / COENZYME A / GLYCYL-ADENOSINE-5'-PHOSPHATE / 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. / Luic, M. / Mocibob, M. / Ivic, N. / Subasic, D.
Citation
Journal: Croatica Chemica Acta / Year: 2011
Title: Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases
Authors: Mocibob, M. / Ivic, N. / Subasic, D. / Luic, M. / Weygand-Durasevic, I.
#1: 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.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Amino acid--[acyl-carrier-protein] ligase 1
B: Amino acid--[acyl-carrier-protein] ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98211
Polymers76,3182
Non-polymers1,6649
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-40 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.194, 101.791, 50.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amino acid--[acyl-carrier-protein] ligase 1 / Amino acid:[carrier-protein] ligase [AMP forming] 1 / aa:CP ligase 1 / Aminoacyl-[acyl-carrier- ...Amino acid:[carrier-protein] ligase [AMP forming] 1 / aa:CP ligase 1 / Aminoacyl-[acyl-carrier-protein] synthetase 1 / L-glycine:[acyl-carrier-protein] ligase 1


Mass: 38159.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: bll0957 / Production host: Escherichia coli (E. coli)
References: UniProt: Q89VT8, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases

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Non-polymers , 6 types, 331 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GAP / GLYCYL-ADENOSINE-5'-PHOSPHATE


Mass: 404.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N6O8P
#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: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.17M ammonium acetate, 0.085M sodium acetate trihydrate, 25.5% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, 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: Jan 28, 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→20.86 Å / Num. all: 34431 / Num. obs: 32404 / % possible obs: 99.85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.95 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.6755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique all% possible all
2.2-2.323.170.441.7515675495299.89
2.32-2.463.420.332.2715966466899.98
2.46-2.634.090.262.9118059441899.94
2.63-2.844.680.194.06193774141100
2.84-3.115.010.135.76191073813100
3.11-3.485.550.089.19192193464100
3.48-4.026.910.0513.72212853081100
4.02-4.927.320.0321.92193572645100
4.92-6.967.140.0320.68147902072100
6.96-20.866.440.0231.317576117796

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CrysalisProProdata collection
CrysalisProdata reduction
REFMAC5.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→20.86 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 1.88 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1605 4.95 %RANDOM
Rwork0.167 ---
all0.1698 34460 --
obs0.1698 32404 94.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.832 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 103.64 Å2 / Biso mean: 26.3009 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.4663 Å20 Å2-0 Å2
2--3.9168 Å20 Å2
3----2.7701 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 0 88 322 4872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074799
X-RAY DIFFRACTIONf_angle_d1.0416527
X-RAY DIFFRACTIONf_chiral_restr0.068688
X-RAY DIFFRACTIONf_plane_restr0.005860
X-RAY DIFFRACTIONf_dihedral_angle_d18.9761756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27090.31381280.24562543267187
2.2709-2.3520.28361290.20392598272789
2.352-2.4460.25431350.18552607274289
2.446-2.55720.24651460.17462679282591
2.5572-2.69170.24411450.17192758290394
2.6917-2.860.21941480.16452785293395
2.86-3.08020.20781450.16992840298596
3.0802-3.38890.23091550.15582928308398
3.3889-3.87660.1941520.15112956310899
3.8766-4.87380.16831580.12652969312799
4.8738-20.86360.21471640.15873136330099

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