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- PDB-6m2t: The crystal structure of benzoate coenzyme A ligase double mutant... -

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Basic information

Entry
Database: PDB / ID: 6m2t
TitleThe crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE
Function / homology
Function and homology information


CoA-ligase activity / 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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
2-methyl-1,3-thiazole-5-carboxylic acid / ADENOSINE MONOPHOSPHATE / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLi, T.L. / Adhikari, K.
CitationJournal: To Be Published
Title: The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP
Authors: Li, T.L. / Adhikari, K. / Malek, Z.S.
History
DepositionFeb 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Benzoate-coenzyme A ligase
D: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,69412
Polymers226,7324
Non-polymers1,9628
Water24,8071377
1
A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1733
Polymers56,6831
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1733
Polymers56,6831
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1733
Polymers56,6831
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1733
Polymers56,6831
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.046, 95.143, 119.524
Angle α, β, γ (deg.)90.00, 110.58, 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.: 4 / 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: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-6V9 / 2-methyl-1,3-thiazole-5-carboxylic acid


Type: peptide linking / Mass: 143.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1377 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
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: 2.138→27.783 Å / Num. obs: 113090 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 25.33
Reflection shellResolution: 2.14→2.22 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 113090 / % possible all: 100

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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: 6M20

6m20


Resolution: 2.14→27.78 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2003 1.77 %
Rwork0.16 --
obs0.16 113090 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15608 0 124 1377 17109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716211
X-RAY DIFFRACTIONf_angle_d0.97722160
X-RAY DIFFRACTIONf_dihedral_angle_d13.4799627
X-RAY DIFFRACTIONf_chiral_restr0.0662470
X-RAY DIFFRACTIONf_plane_restr0.0062883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.1910.22881280.17717433X-RAY DIFFRACTION94
2.191-2.25030.22531500.1687922X-RAY DIFFRACTION100
2.2503-2.31640.19821360.16468008X-RAY DIFFRACTION100
2.3164-2.39120.22121450.16477955X-RAY DIFFRACTION100
2.3912-2.47660.21761440.1667910X-RAY DIFFRACTION100
2.4766-2.57570.17321430.16537978X-RAY DIFFRACTION100
2.5757-2.69280.22831450.17087911X-RAY DIFFRACTION100
2.6928-2.83460.23971360.17417971X-RAY DIFFRACTION100
2.8346-3.0120.22281480.17637938X-RAY DIFFRACTION100
3.012-3.24430.19821460.1718007X-RAY DIFFRACTION100
3.2443-3.57020.18531450.15537987X-RAY DIFFRACTION100
3.5702-4.08540.18451420.14398006X-RAY DIFFRACTION100
4.0854-5.14180.15851440.13518010X-RAY DIFFRACTION100
5.1418-27.780.19891510.16268051X-RAY DIFFRACTION99

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