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- PDB-4h2v: Crystal structure of Bradyrhizobium japonicum glycine:[carrier pr... -

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Basic information

Entry
Database: PDB / ID: 4h2v
TitleCrystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with glycylated carrier protein
Components
  • Amino acid--[acyl-carrier-protein] ligase 1
  • Aminoacyl carrier protein 1
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 / lipid A biosynthetic process / acyl binding / acyl carrier activity / ATP binding / metal ion binding / membrane / cytosol
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
ACETATE ION / ADENOSINE MONOPHOSPHATE / Chem-H2V / 4'-PHOSPHOPANTETHEINE / PHOSPHATE ION / Aminoacyl carrier protein 1 / Amino acid--[acyl-carrier-protein] ligase 1
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
C: Aminoacyl carrier protein 1
D: Aminoacyl carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,70717
Polymers100,5524
Non-polymers2,15513
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-186 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.853, 101.020, 104.407
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: 38159.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll0957 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q89VT8, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Protein Aminoacyl carrier protein 1


Mass: 12116.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bsr0959 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89VT6

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Non-polymers , 9 types, 350 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-H2V / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] aminoethanethioate / S-glycyl-4'-phosphopantetheine


Mass: 415.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26N3O8PS
#10: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5% PEG 8000, 0.17M ammonium sulfate, 0.085 M sodium cacodylate pH 6.5, 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: 0.95374 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2→46.38 Å / Num. all: 65834 / Num. obs: 65485 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36.469 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.120.4744.627462410230197.5
2.12-2.260.3087.07734769872199.9
2.26-2.450.19710.58686479215199.9
2.45-2.680.13414.866342285231100
2.68-2.990.07923.25571987696199.9
2.99-3.450.04835.9505036844199.9
3.45-4.220.03350.21426475848199.9
4.22-5.950.02859.15329604581199.9
5.95-46.380.02560.68182312676199.4

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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→46.38 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.2 / σ(F): 1.99 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 3296 5.03 %RANDOM
Rwork0.1794 ---
obs0.1809 65482 99.51 %-
all-65834 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.06 Å2 / Biso mean: 32.6306 Å2 / Biso min: 7.45 Å2
Refinement stepCycle: LAST / Resolution: 2→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 127 337 5724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075635
X-RAY DIFFRACTIONf_angle_d1.0457680
X-RAY DIFFRACTIONf_chiral_restr0.071844
X-RAY DIFFRACTIONf_plane_restr0.0051030
X-RAY DIFFRACTIONf_dihedral_angle_d12.872093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02580.25121360.22662307244390
2.0258-2.05610.23111550.199325682723100
2.0561-2.08820.23831350.188525482683100
2.0882-2.12240.27061300.183625722702100
2.1224-2.1590.24151300.185925762706100
2.159-2.19830.23381450.187825832728100
2.1983-2.24060.21561240.188425562680100
2.2406-2.28630.20261360.186925932729100
2.2863-2.3360.2141360.177925702706100
2.336-2.39040.2591380.177725802718100
2.3904-2.45010.25681370.176925852722100
2.4501-2.51640.21521360.178525932729100
2.5164-2.59040.19321350.179725922727100
2.5904-2.6740.22241330.180725942727100
2.674-2.76960.22431330.177225942727100
2.7696-2.88050.18231480.174125712719100
2.8805-3.01150.22441250.181426122737100
3.0115-3.17030.23461400.179326132753100
3.1703-3.36890.2011400.171226222762100
3.3689-3.62890.18731370.171726032740100
3.6289-3.99390.18081410.162926332774100
3.9939-4.57140.17121380.157226462784100
4.5714-5.75770.19231400.171226792819100
5.7577-46.380.24011480.217827962944100

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