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- PDB-6m2o: Double mutant(H333A/I334A) crystal structure of benzoate coenzyme... -

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Basic information

Entry
Database: PDB / ID: 6m2o
TitleDouble mutant(H333A/I334A) crystal structure of benzoate coenzyme A ligase
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE
Function / homology
Function and homology information


acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
Benzoate-CoA ligase family / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLi, T.L. / Adhikari, K.
CitationJournal: Biomolecules / Year: 2020
Title: Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase.
Authors: Adhikari, K. / Lo, I.W. / Chen, C.L. / Wang, Y.L. / Lin, K.H. / Zadeh, S.M. / Rattinam, R. / Li, Y.S. / Wu, C.J. / Li, T.L.
History
DepositionFeb 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzoate-coenzyme A ligase
B: Benzoate-coenzyme A ligase


Theoretical massNumber of molelcules
Total (without water)113,3662
Polymers113,3662
Non-polymers00
Water21,2581180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-5 kcal/mol
Surface area38330 Å2
Unit cell
Length a, b, c (Å)59.115, 95.379, 94.989
Angle α, β, γ (deg.)90.00, 105.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56683.098 Da / Num. of mol.: 2 / Mutation: T83A, H333A, I334A, G341D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: badA / Production host: Rhodopseudomonas palustris (phototrophic) / References: UniProt: Q93TK0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1180 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, 0.1 M sodium chloride, 0.2 M MES pH 6.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→29.516 Å / Num. obs: 140471 / % possible obs: 99.12 % / Redundancy: 3.8 % / CC1/2: 0.904 / Net I/σ(I): 32.95
Reflection shellResolution: 1.57→1.57 Å / CC1/2: 0.904 / CC star: 0.974 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EAT

4eat


Resolution: 1.57→29.516 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.2116 2006 1.43 %
Rwork0.1872 --
obs0.1875 140471 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→29.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7804 0 0 1180 8984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078040
X-RAY DIFFRACTIONf_angle_d0.90710982
X-RAY DIFFRACTIONf_dihedral_angle_d6.8726450
X-RAY DIFFRACTIONf_chiral_restr0.0551226
X-RAY DIFFRACTIONf_plane_restr0.0061436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60910.26481370.22979500X-RAY DIFFRACTION96
1.6091-1.65260.23951460.21619808X-RAY DIFFRACTION99
1.6526-1.70120.22991370.20969871X-RAY DIFFRACTION99
1.7012-1.75610.24321540.21449795X-RAY DIFFRACTION99
1.7561-1.81890.25791350.2129882X-RAY DIFFRACTION99
1.8189-1.89170.24471420.20559864X-RAY DIFFRACTION99
1.8917-1.97780.23191420.20449951X-RAY DIFFRACTION99
1.9778-2.0820.20951470.19479878X-RAY DIFFRACTION99
2.082-2.21240.22931440.19239926X-RAY DIFFRACTION100
2.2124-2.38320.23021410.19049995X-RAY DIFFRACTION100
2.3832-2.62290.22891450.19389935X-RAY DIFFRACTION100
2.6229-3.00210.19361430.19199980X-RAY DIFFRACTION100
3.0021-3.78110.18751450.166710003X-RAY DIFFRACTION100
3.7811-29.5160.1721480.156810077X-RAY DIFFRACTION99

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