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- PDB-5bsv: Crystal structure of 4-coumarate:CoA ligase complexed with ferulo... -

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Basic information

Entry
Database: PDB / ID: 5bsv
TitleCrystal structure of 4-coumarate:CoA ligase complexed with feruloyl adenylate
Components4-coumarate--CoA ligase 2
KeywordsLIGASE / 4-coumarate:CoA ligase
Function / homology
Function and homology information


trans-feruloyl-CoA synthase activity / trans-cinnamate-CoA ligase activity / trans-feruloyl-CoA synthase / 4-coumarate-CoA ligase activity / (E)-caffeate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid ...trans-feruloyl-CoA synthase activity / trans-cinnamate-CoA ligase activity / trans-feruloyl-CoA synthase / 4-coumarate-CoA ligase activity / (E)-caffeate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid / response to wounding / ATP binding
Similarity search - Function
ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4UW / 4-coumarate--CoA ligase 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLi, Z. / Nair, S.K.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase.
Authors: Li, Z. / Nair, S.K.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0692
Polymers59,5461
Non-polymers5231
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.441, 82.441, 181.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 4-coumarate--CoA ligase 2 / 4CL 2 / 4-coumaroyl-CoA synthase 2


Mass: 59545.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: 4CL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O24146, 4-coumarate-CoA ligase
#2: Chemical ChemComp-4UW / 5'-O-[(R)-hydroxy{[(2E)-3-(5-methoxy-4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine


Mass: 523.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N5O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5% w/v PEG 8000, 0.085 M sodium cacodylate pH 6.5, 0.17 M sodium acetate, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97947 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 69481 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.92 / Net I/av σ(I): 41.545 / Net I/σ(I): 11.1 / Num. measured all: 498995
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.766.90.49968411.26799.8
1.76-1.837.20.38768601.282100
1.83-1.917.30.28168601.349100
1.91-2.027.30.20468901.497100
2.02-2.147.30.15268771.76100
2.14-2.317.30.12469202.06499.9
2.31-2.547.30.09869431.96499.9
2.54-2.917.30.07869732.09699.7
2.91-3.667.10.06670402.98799.3
3.66-506.90.05172772.89397.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0056refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.683 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 3503 5.1 %RANDOM
Rwork0.1894 ---
obs0.1903 65759 99.61 %-
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 max: 49.84 Å2 / Biso mean: 24.057 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4081 0 36 316 4433
Biso mean--17.62 32.13 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224204
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9925709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3335528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96624.97169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30115727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2961517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213128
X-RAY DIFFRACTIONr_mcbond_it0.4431.52644
X-RAY DIFFRACTIONr_mcangle_it0.89124296
X-RAY DIFFRACTIONr_scbond_it1.61531560
X-RAY DIFFRACTIONr_scangle_it2.7294.51413
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 252 -
Rwork0.208 4780 -
all-5032 -
obs--99.74 %

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