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- PDB-5bst: Crystal structure of 4-coumarate:CoA ligase complexed with coumar... -

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Basic information

Entry
Database: PDB / ID: 5bst
TitleCrystal structure of 4-coumarate:CoA ligase complexed with coumaroyl 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-4UU / 4-coumarate--CoA ligase 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.61 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)60,0633
Polymers59,5461
Non-polymers5182
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.830, 81.830, 180.988
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-4UU / 5'-O-[(R)-hydroxy{[(2E)-3-(4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine


Mass: 493.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N5O9P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4% (w/v) PEG 8000, 0.08 M sodium cacodylate pH 6.5, 0.16 M calcium acetate, and 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 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: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 79566 / % possible obs: 99 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.082 / Χ2: 1.389 / Net I/av σ(I): 47.828 / Net I/σ(I): 9.5 / Num. measured all: 1259529
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.61-1.6713.90.43577380.74198.1
1.67-1.7315.50.3577670.76898.4
1.73-1.8115.80.27178140.8298.5
1.81-1.9116.10.19778320.91998.8
1.91-2.0316.30.14478671.05899
2.03-2.1916.40.10979101.23499.2
2.19-2.416.40.09179861.41299.4
2.4-2.7516.40.07980031.60799.5
2.75-3.4716.10.07181282.46199.8
3.47-5015.30.05485212.65299.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.61→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.451 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 3988 5 %RANDOM
Rwork0.1991 ---
obs0.1999 75523 99.03 %-
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: 67.68 Å2 / Biso mean: 18.603 Å2 / Biso min: 8 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.61→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 35 503 4618
Biso mean--10.11 30.47 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194201
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.995705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78824.97169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0215726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213127
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 279 -
Rwork0.241 5392 -
all-5671 -
obs--97.62 %

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