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- PDB-5bsr: Crystal structure of 4-coumarate:CoA ligase complexed with adenos... -

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Basic information

Entry
Database: PDB / ID: 5bsr
TitleCrystal structure of 4-coumarate:CoA ligase complexed with adenosine monophosphate and Coenzyme A
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
ADENOSINE MONOPHOSPHATE / COENZYME A / 4-coumarate--CoA ligase 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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)61,0297
Polymers59,5461
Non-polymers1,4836
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.898, 82.092, 97.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97621 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: 0.97621 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 87642 / % possible obs: 96.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.065 / Χ2: 1.527 / Net I/av σ(I): 41.833 / Net I/σ(I): 11.7 / Num. measured all: 725691
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.554.10.49368090.84376.2
1.55-1.626.70.46484080.84594.3
1.62-1.697.90.35788710.89799.1
1.69-1.788.70.26689030.96399.8
1.78-1.898.90.18289931.12599.9
1.89-2.0490.12689801.426100
2.04-2.249.10.0990151.736100
2.24-2.569.30.0790811.827100
2.56-3.239.20.0691392.389100
3.23-508.90.04294432.29299.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.253 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 4380 5 %RANDOM
Rwork0.1879 ---
obs0.1891 83093 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 96.74 Å2 / Biso mean: 22.592 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å2-0 Å2-0 Å2
2---1.17 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 95 527 4698
Biso mean--29.15 31.9 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194264
X-RAY DIFFRACTIONr_angle_refined_deg1.2622.0045792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08424.941170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45515728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.521517
X-RAY DIFFRACTIONr_chiral_restr0.1280.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213138
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 248 -
Rwork0.277 4705 -
all-4953 -
obs--75.53 %

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