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- PDB-4zjz: Crystal structure of a benzoate coenzyme A ligase with Benzoyl-AMP -

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Basic information

Entry
Database: PDB / ID: 4zjz
TitleCrystal structure of a benzoate coenzyme A ligase with Benzoyl-AMP
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Substrate Specificity / Kinetics
Function / homology
Function and homology information


benzoate-CoA ligase / benzoate-CoA ligase activity / 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
BENZOIC ACID / Chem-OOB / Benzoate-CoA ligase / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Data collection / Database references
Revision 1.2Oct 28, 2015Group: Data collection / Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)115,65216
Polymers113,5842
Non-polymers2,06814
Water11,656647
1
A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7347
Polymers56,7921
Non-polymers9426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9189
Polymers56,7921
Non-polymers1,1268
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.615, 95.611, 95.706
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56792.246 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, UniProt: Q6NC13*PLUS
#2: Chemical ChemComp-OOB / 5'-O-[(R)-(benzoyloxy)(hydroxy)phosphoryl]adenosine


Type: RNA OH 5 prime terminus / Mass: 451.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N5O8P
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15 % PEG 3350, 0.1 M Tris pH 7.0

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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: 1.7→50 Å / Num. obs: 112317 / % possible obs: 96.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.088 / Rsym value: 0.069 / Net I/σ(I): 17.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2 / % possible all: 84.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7B

2v7b


Resolution: 1.7→29.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.867 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19204 5437 5 %RANDOM
Rwork0.15175 ---
obs0.15375 103134 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.7→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7842 0 140 647 8629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0228228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.261.98111222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29251048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9222.81331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.195151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8871557
X-RAY DIFFRACTIONr_chiral_restr0.2010.21235
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216335
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.431.55184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26928299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.64433044
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7554.52916
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 329 -
Rwork0.239 6406 -
obs--81.37 %

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