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- PDB-4h2y: Crystal structure of engineered Bradyrhizobium japonicum glycine:... -

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Basic information

Entry
Database: PDB / ID: 4h2y
TitleCrystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and ATP
Components
  • Amino acid--[acyl-carrier-protein] ligase 1
  • Aminoacyl carrier protein
KeywordsLIGASE / ATP binding / glycine binding / carrier protein / aminoacyl-tRNA synthetase / seryl-tRNA synthetase
Function / homology
Function and homology information


: / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ligase activity / ATP binding / metal ion binding
Similarity search - Function
ACP-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. ...ACP-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4'-PHOSPHOPANTETHEINE / Aminoacyl carrier protein / Amino acid--[acyl-carrier-protein] ligase / Amino acid--[acyl-carrier-protein] ligase 1
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
Agrobacterium fabrum (bacteria)
Agrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLuic, M. / Weygand-Durasevic, I. / Ivic, N. / Mocibob, M.
Citation
Journal: Structure / Year: 2013
Title: Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation.
Authors: Mocibob, M. / Ivic, N. / 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
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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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
C: Aminoacyl carrier protein
D: Aminoacyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,56411
Polymers98,6774
Non-polymers1,8867
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-182 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.863, 101.587, 103.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Amino acid--[acyl-carrier-protein] ligase 1 / Aminoacyl-[acyl-carrier-protein] synthetase 1


Mass: 38173.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria), (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: USDA 110 / Gene: bll0957, Atu2573,AGR_C_4663 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q89VT8, UniProt: Q7CWR3, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Protein Aminoacyl carrier protein


Mass: 11165.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4658, Atu2571 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CHM9

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Non-polymers , 5 types, 378 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAINS A, B ARE CHIMERIC PROTEINS COMPOSED OF UNP RESIDUES Q89VT8 1-220, Q7CWR3 236-246, Q89VT8 232-326

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 4000, 10% PEG 8000, 0.17M ammonium acetate, 0.085M trisodium citrate dyhydrate pH 5.6, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→46.08 Å / Num. all: 62151 / Num. obs: 62048 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 38.841 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.230.6333.07606609881199.5
2.23-2.380.3895.02577669326199.9
2.38-2.570.2557.355392886711100
2.57-2.810.16211.174973780361100
2.81-3.140.09218.474512573071100
3.14-3.630.05429392746451199.9
3.63-4.440.03541.64330705512199.9
4.44-6.250.02850.23254374328199.8
6.25-46.080.02156.01140592535199.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1116refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→46.08 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.21 / σ(F): 1.99 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 3101 5 %RANDOM
Rwork0.1762 ---
obs0.1779 62041 99.83 %-
all-62151 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.95 Å2 / Biso mean: 37.6035 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 107 371 5987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075861
X-RAY DIFFRACTIONf_angle_d1.0687997
X-RAY DIFFRACTIONf_chiral_restr0.067875
X-RAY DIFFRACTIONf_plane_restr0.0061073
X-RAY DIFFRACTIONf_dihedral_angle_d12.7042158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13180.26261400.2272629276998
2.1318-2.16670.23911370.209226462783100
2.1667-2.20410.25671390.215826542793100
2.2041-2.24420.24931400.214226472787100
2.2442-2.28730.26041370.214326212758100
2.2873-2.3340.2541370.201326592796100
2.334-2.38480.21551460.186626492795100
2.3848-2.44020.25571360.182226642800100
2.4402-2.50120.22551390.185626472786100
2.5012-2.56890.2181410.182526552796100
2.5689-2.64450.2591400.187526742814100
2.6445-2.72980.24431410.182726622803100
2.7298-2.82740.21161400.180326652805100
2.8274-2.94050.24361420.178426772819100
2.9405-3.07430.20541400.178126782818100
3.0743-3.23640.21861420.173226842826100
3.2364-3.43910.19561410.171326872828100
3.4391-3.70450.21491420.16626872829100
3.7045-4.07710.17951420.156827042846100
4.0771-4.66660.16511440.137227292873100
4.6666-5.87750.19641430.169627532896100
5.8775-46.080.19251520.18932869302199

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