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- PDB-4h2s: Crystal structure of Bradyrhizobium japonicum glycine:[carrier pr... -

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Basic information

Entry
Database: PDB / ID: 4h2s
TitleCrystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and AMP
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 / 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 / 4'-PHOSPHOPANTETHEINE / Aminoacyl carrier protein 1 / Amino acid--[acyl-carrier-protein] ligase 1
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)102,15311
Polymers100,5524
Non-polymers1,6017
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-169 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.046, 101.677, 103.981
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, 425 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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 418 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
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: 1.0051 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: 1.0051 Å / Relative weight: 1
ReflectionResolution: 2.15→46.29 Å / Num. all: 53912 / Num. obs: 53843 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36.369 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.280.5284.2637178563199.7
2.28-2.430.3476.286050780631100
2.43-2.630.2458.875672975561100
2.63-2.880.15113.755221469551100
2.88-3.220.08622.554740563251100
3.22-3.710.04936.774180156151100
3.71-4.540.03153.273526947791100
4.54-6.390.02758.772735337701100
6.39-46.290.01971.74151982217199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMRphasing
PHENIXdev_1116refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MF2

3mf2


Resolution: 2.15→46.29 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.2 / σ(F): 2 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2692 5 %RANDOM
Rwork0.1705 ---
obs0.1723 53840 99.92 %-
all-53843 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.19 Å2 / Biso mean: 31.5696 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 94 418 5849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085687
X-RAY DIFFRACTIONf_angle_d1.0477749
X-RAY DIFFRACTIONf_chiral_restr0.069850
X-RAY DIFFRACTIONf_plane_restr0.0051044
X-RAY DIFFRACTIONf_dihedral_angle_d13.2062124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.18710.24611380.20182622276099
2.1871-2.22910.22141400.190826472787100
2.2291-2.27460.26541400.179126742814100
2.2746-2.32410.24991400.181826582798100
2.3241-2.37820.24381400.171126482788100
2.3782-2.43760.20711410.17626792820100
2.4376-2.50350.21061400.17526582798100
2.5035-2.57720.23941400.170526662806100
2.5772-2.66040.25581400.177226692809100
2.6604-2.75540.21641410.170126782819100
2.7554-2.86580.19111420.156526872829100
2.8658-2.99620.19571400.165726672807100
2.9962-3.15410.21111430.167227052848100
3.1541-3.35160.2161410.161926932834100
3.3516-3.61030.18521420.162827022844100
3.6103-3.97350.20541430.155927092852100
3.9735-4.5480.17521440.146827352879100
4.548-5.72830.16571460.163927652911100
5.7283-46.290.22241510.212428863037100

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