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- PDB-4h2t: Crystal structure of Bradyrhizobium japonicum glycine:[carrier pr... -

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Basic information

Entry
Database: PDB / ID: 4h2t
TitleCrystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and an analogue of glycyl adenylate
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
5'-O-(glycylsulfamoyl)adenosine / 4'-PHOSPHOPANTETHEINE / 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: 2.44 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 1.3Jun 19, 2013Group: Atomic model
Revision 1.4Mar 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_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_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.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)102,39812
Polymers100,5524
Non-polymers1,8468
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-120 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.461, 101.218, 104.654
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 / 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) / 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 , 5 types, 223 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N7O7S
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


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


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.94 %
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: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.44→46.49 Å / Num. all: 36794 / Num. obs: 36621 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 43.465 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 46.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.44-2.590.593.5422065757198.6
2.59-2.770.4095.18410275504199.8
2.77-2.990.2498.27381065121199.8
2.99-3.270.15213.263518747431100
3.27-3.660.08722.273183943071100
3.66-4.220.05334.41280513818199.9
4.22-5.160.03648.582361732501100
5.16-7.250.03944.091848625881100

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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: 2.44→46.49 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.28 / σ(F): 1.99 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1833 5.01 %RANDOM
Rwork0.1783 ---
obs0.1802 36621 99.72 %-
all-36794 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.71 Å2 / Biso mean: 29.6736 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.44→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 108 215 5579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085502
X-RAY DIFFRACTIONf_angle_d1.1287484
X-RAY DIFFRACTIONf_chiral_restr0.07825
X-RAY DIFFRACTIONf_plane_restr0.0051003
X-RAY DIFFRACTIONf_dihedral_angle_d13.2972019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.44-2.50880.27911340.20712580271497
2.5088-2.58260.29551370.204426502787100
2.5826-2.6660.27511450.20326142759100
2.666-2.76120.24171320.197126542786100
2.7612-2.87180.23591430.180226502793100
2.8718-3.00250.25651410.18826462787100
3.0025-3.16070.22631440.183326702814100
3.1607-3.35870.23181390.173326622801100
3.3587-3.61790.20351400.17726732813100
3.6179-3.98180.20451400.163226892829100
3.9818-4.55760.17541440.153327182862100
4.5576-5.74040.19291420.161927222864100
5.7404-46.490.20891520.200128603012100

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