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- PDB-6m2u: The crystal structure of benzoate coenzyme A ligase double mutant... -

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Basic information

Entry
Database: PDB / ID: 6m2u
TitleThe crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-chloro-1,3-thiazole-5-carboxylate-AMP
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Benzoate / coenzyme / complex
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
ADENOSINE MONOPHOSPHATE / 2-chloranyl-1,3-thiazole-5-carboxylic acid / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 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 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3576
Polymers112,3352
Non-polymers1,0224
Water23,5461307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-6 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.524, 94.656, 94.355
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56167.500 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: Escherichia coli (E. coli) / References: UniProt: Q93TK0
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-F0O / 2-chloranyl-1,3-thiazole-5-carboxylic acid


Mass: 163.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H2ClNO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, 0.1 M sodium chloride, 0.2 M MES

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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: 1.709→29.816 Å / Num. obs: 105468 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.97 / Net I/σ(I): 33.03
Reflection shellResolution: 1.709→1.709 Å / Num. unique obs: 105468 / CC1/2: 0.887

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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: 6M2O

6m2o


Resolution: 1.709→29.816 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 1996 1.89 %
Rwork0.1695 --
obs0.1702 105468 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.709→29.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7827 0 62 1307 9196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068107
X-RAY DIFFRACTIONf_angle_d1.01711070
X-RAY DIFFRACTIONf_dihedral_angle_d12.4684742
X-RAY DIFFRACTIONf_chiral_restr0.0811230
X-RAY DIFFRACTIONf_plane_restr0.0061438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.709-1.75170.3231000.25246028X-RAY DIFFRACTION81
1.7517-1.7990.29511450.22247211X-RAY DIFFRACTION96
1.799-1.8520.23071520.20367495X-RAY DIFFRACTION99
1.852-1.91170.22381420.19437455X-RAY DIFFRACTION100
1.9117-1.980.23561470.19267487X-RAY DIFFRACTION100
1.98-2.05930.23011470.18057511X-RAY DIFFRACTION100
2.0593-2.1530.22071480.17337503X-RAY DIFFRACTION100
2.153-2.26650.20551360.16727524X-RAY DIFFRACTION100
2.2665-2.40840.20911470.16837461X-RAY DIFFRACTION100
2.4084-2.59430.2051480.177517X-RAY DIFFRACTION100
2.5943-2.85510.23131470.17367538X-RAY DIFFRACTION100
2.8551-3.26780.2031440.16787569X-RAY DIFFRACTION100
3.2678-4.11540.16961430.14267541X-RAY DIFFRACTION100
4.1154-29.8160.15991500.14577632X-RAY DIFFRACTION100

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