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- PDB-9s3l: ClxA from Clostridium cavendishii (apo) -

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Basic information

Entry
Database: PDB / ID: 9s3l
TitleClxA from Clostridium cavendishii (apo)
ComponentsPhenylacetate-CoA ligase
KeywordsLIGASE / ATP / amide / closoxazole
Function / homologyANL, N-terminal domain / ligase activity / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phenylacetate-CoA ligase
Function and homology information
Biological speciesClostridium cavendishii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsAscham, A. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Biocatalytic synthesis of phenyl benzoate esters using the amide ligase ClxA.
Authors: Ascham, A. / Tang, Q. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylacetate-CoA ligase
B: Phenylacetate-CoA ligase
C: Phenylacetate-CoA ligase
D: Phenylacetate-CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,69411
Polymers180,3604
Non-polymers3357
Water1,40578
1
A: Phenylacetate-CoA ligase
B: Phenylacetate-CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3596
Polymers90,1802
Non-polymers1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-62 kcal/mol
Surface area31910 Å2
MethodPISA
2
C: Phenylacetate-CoA ligase
D: Phenylacetate-CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3355
Polymers90,1802
Non-polymers1553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-53 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.940, 79.970, 81.770
Angle α, β, γ (deg.)90.26, 95.58, 103.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Phenylacetate-CoA ligase


Mass: 45089.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cavendishii (bacteria) / Gene: SAMN02745163_01864 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6IZB6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2; 0.1 M Tris-HCl; 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7338 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7338 Å / Relative weight: 1
ReflectionResolution: 2.57→40.71 Å / Num. obs: 55692 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.17 / Net I/σ(I): 2.8
Reflection shellResolution: 2.57→2.64 Å / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4566 / CC1/2: 0.59 / Rpim(I) all: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→40.71 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.85 / SU B: 35.714 / SU ML: 0.65 / Cross valid method: THROUGHOUT / ESU R: 1.192 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30094 2740 4.9 %RANDOM
Rwork0.26509 ---
obs0.26687 52942 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.25 Å2
Baniso -1Baniso -2Baniso -3
1-7.72 Å21.21 Å21.61 Å2
2---5.89 Å2-0.97 Å2
3----1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.57→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12113 0 7 78 12198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212356
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611725
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.82516770
X-RAY DIFFRACTIONr_angle_other_deg0.5081.74726997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08551590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.614547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.665102022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21975
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022583
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_it3.8334.3346372
X-RAY DIFFRACTIONr_mcbond_other3.8324.3346372
X-RAY DIFFRACTIONr_mcangle_it6.3197.7827958
X-RAY DIFFRACTIONr_mcangle_other6.3187.7837959
X-RAY DIFFRACTIONr_scbond_it3.1394.3365984
X-RAY DIFFRACTIONr_scbond_other3.1374.3365983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3847.998813
X-RAY DIFFRACTIONr_long_range_B_refined8.87741.713513
X-RAY DIFFRACTIONr_long_range_B_other8.87741.7113514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 180 -
Rwork0.381 3867 -
obs--98.8 %

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