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- PDB-3a9v: Crystal structures and enzymatic mechanisms of a Populus tomentos... -

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Basic information

Entry
Database: PDB / ID: 3a9v
TitleCrystal structures and enzymatic mechanisms of a Populus tomentosa 4-coumarate--CoA ligase
Components4-coumarate--CoA ligase
KeywordsLIGASE / 4-coumate--CoA ligase / 4CL / phenylpropanoid pathway
Function / homology
Function and homology information


4-coumarate-CoA ligase / ligase activity / nucleotide 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 / 4-coumarate--CoA ligase
Similarity search - Component
Biological speciesPopulus tomentosa (Chinese white poplar)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.5 Å
AuthorsHu, Y.
CitationJournal: Plant Cell / Year: 2010
Title: Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms
Authors: Hu, Y. / Gai, Y. / Yin, L. / Wang, X. / Feng, C. / Feng, L. / Li, D. / Jiang, X.N. / Wang, D.C.
History
DepositionNov 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9552
Polymers58,6081
Non-polymers3471
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.340, 162.340, 162.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein 4-coumarate--CoA ligase


Mass: 58607.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tomentosa (Chinese white poplar)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q941M3, 4-coumarate-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.04 Å3/Da / Density % sol: 59.56 % / Mosaicity: 0.677 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 20mg/ml of Pt4CL1, 50mM Tris pH 7.5, 10%(v/v) glycerol, 0.1M NaCl, 10mM AMP, 2mM DTT, 1mM EDTA, precipitate solution: 50mM MES pH 6.0, 1.8M ammonium citrate, VAPOR ...Details: Protein solution: 20mg/ml of Pt4CL1, 50mM Tris pH 7.5, 10%(v/v) glycerol, 0.1M NaCl, 10mM AMP, 2mM DTT, 1mM EDTA, precipitate solution: 50mM MES pH 6.0, 1.8M ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 24, 2007 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→114.792 Å / Num. all: 24749 / Num. obs: 24708 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / Num. measured all: 13811 / Num. unique all: 3556 / Rsym value: 0.381 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.8 Å11.97 Å
Translation3.8 Å11.97 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: molecular replacement
Starting model: 3A9U

3a9u


Resolution: 2.5→51.34 Å / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1258 5.1 %random
Rwork0.204 ---
all-24749 --
obs-24675 99.7 %-
Solvent computationBsol: 37.561 Å2
Displacement parametersBiso mean: 28.698 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 23 124 4194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.302
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION44clxd.param
X-RAY DIFFRACTION5amp.param

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