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- PDB-4h2x: Crystal structure of engineered Bradyrhizobium japonicum glycine:... -

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Basic information

Entry
Database: PDB / ID: 4h2x
TitleCrystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate
Components
  • (Amino acid--[acyl-carrier-protein] ligase ...) x 2
  • 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
5'-O-(glycylsulfamoyl)adenosine / 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: 2.15 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
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 1.4Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Mar 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_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_entry_details.has_protein_modification / _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_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
D: Aminoacyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,36911
Polymers98,7094
Non-polymers1,6607
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-124 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.575, 101.433, 103.044
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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Amino acid--[acyl-carrier-protein] ligase ... , 2 types, 2 molecules AB

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


Mass: 38205.145 Da / Num. of mol.: 1
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 Amino acid--[acyl-carrier-protein] ligase 1 / Aminoacyl-[acyl-carrier-protein] synthetase 1


Mass: 38173.145 Da / Num. of mol.: 1
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

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Protein , 1 types, 2 molecules CD

#3: 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, 354 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


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


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 2.64 Å3/Da / Density % sol: 53.34 %
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: ID29 / Wavelength: 1.28215 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 2.15→45.94 Å / Num. all: 57783 / Num. obs: 57632 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 42.014 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 31.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.280.4365.11021259086198.5
2.28-2.430.2719.0811683286661100
2.43-2.630.18512.7910507280851100
2.63-2.880.11520.6310143074601100
2.88-3.210.0732.558793567921100
3.21-3.710.04651.78072760091100
3.71-4.530.03171.686598751241100
4.53-6.380.02877.1509364034199.9
6.38-45.940.02488.7290162376199.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1116refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→45.94 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.19 / σ(F): 2 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 2878 4.99 %RANDOM
Rwork0.1666 ---
obs0.1681 57625 99.74 %-
all-57783 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.74 Å2 / Biso mean: 41.1123 Å2 / Biso min: 13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 99 347 6092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086058
X-RAY DIFFRACTIONf_angle_d1.0628277
X-RAY DIFFRACTIONf_chiral_restr0.068906
X-RAY DIFFRACTIONf_plane_restr0.0051123
X-RAY DIFFRACTIONf_dihedral_angle_d12.692259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.18070.25151250.21522458258395
2.1807-2.21830.20641400.194625852725100
2.2183-2.25860.26621300.181325942724100
2.2586-2.30210.20421410.168125622703100
2.3021-2.34910.20871330.169725782711100
2.3491-2.40010.1841370.160925662703100
2.4001-2.4560.21331360.167526002736100
2.456-2.51740.22441370.170325812718100
2.5174-2.58540.22571350.175626022737100
2.5854-2.66150.24371360.168525932729100
2.6615-2.74740.21531380.175525782716100
2.7474-2.84560.21881360.174426142750100
2.8456-2.95950.22111370.174425902727100
2.9595-3.09420.18191380.170426122750100
3.0942-3.25730.21831380.168326082746100
3.2573-3.46130.19461350.170326202755100
3.4613-3.72840.21231400.163426322772100
3.7284-4.10340.16841380.152926362774100
4.1034-4.69670.15921400.134826422782100
4.6967-5.91530.18681410.164726892830100
5.9153-45.940.1891470.183628072954100

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