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- PDB-4rlq: Crystal structure of a benzoate coenzyme A ligase with o-Toluic acid -

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Basic information

Entry
Database: PDB / ID: 4rlq
TitleCrystal structure of a benzoate coenzyme A ligase with o-Toluic acid
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Substrate Specificity / Kinetics
Function / homology
Function and homology information


acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-methylbenzoic acid / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsStrom, S. / Nosrati, M. / Thornburg, C. / Walker, K.D. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity.
Authors: Thornburg, C.K. / Wortas-Strom, S. / Nosrati, M. / Geiger, J.H. / Walker, K.D.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references / Structure summary
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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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)113,76913
Polymers112,6672
Non-polymers1,10111
Water10,377576
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A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6544
Polymers56,3341
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1159
Polymers56,3341
Non-polymers7818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.659, 94.808, 95.346
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56333.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: badA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93TK0
#2: Chemical ChemComp-3SK / 2-methylbenzoic acid


Mass: 136.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 442714 / Num. obs: 115478 / % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.055 / Net I/σ(I): 17.1
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.35 / Rsym value: 0.44 / % possible all: 74.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MolRepmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MolRepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→33.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.02 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19312 6135 5 %RANDOM
Rwork0.15812 ---
obs0.15991 115443 96.89 %-
all-442714 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.264 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7884 0 74 576 8534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198224
X-RAY DIFFRACTIONr_bond_other_d0.0010.027764
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.97211214
X-RAY DIFFRACTIONr_angle_other_deg0.944317843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21951051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80522.878337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.035151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9161558
X-RAY DIFFRACTIONr_chiral_restr0.1330.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021880
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8551.9344180
X-RAY DIFFRACTIONr_mcbond_other1.8551.9344179
X-RAY DIFFRACTIONr_mcangle_it2.6042.8925233
X-RAY DIFFRACTIONr_mcangle_other2.6362.8775218
X-RAY DIFFRACTIONr_scbond_it2.972.2214044
X-RAY DIFFRACTIONr_scbond_other2.9462.2084033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3593.1985964
X-RAY DIFFRACTIONr_long_range_B_refined5.71416.2729425
X-RAY DIFFRACTIONr_long_range_B_other5.622169198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 327 -
Rwork0.285 6534 -
obs--74.31 %

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