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- PDB-3a9u: Crystal structures and enzymatic mechanisms of a Populus tomentos... -

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Basic information

Entry
Database: PDB / ID: 3a9u
TitleCrystal structures and enzymatic mechanisms of a Populus tomentosa 4-coumarate--CoA ligase
Components4-coumarate--CoA ligase
KeywordsLIGASE / enzymatic mechanism / phenylpropanoid pathway / 4-coumarate--CoA ligase
Function / homology
Function and homology information


4-coumarate-CoA ligase / 4-coumarate-CoA ligase activity / nucleotide binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-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 ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-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, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-coumarate--CoA ligase
Similarity search - Component
Biological speciesPopulus tomentosa (Chinese white poplar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.4 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-coumarate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)58,6081
Polymers58,6081
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.738, 78.739, 118.787
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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein solution: 50mM Tris pH 7.5, 10%(v/v) glycerol, 0.1M NaCl, 2mM DTT, 1mM EDTA, precipitate solution: 50mM CAPSO pH 9.8, 35%(w/v) PEG8000, 0.25M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9791
SYNCHROTRONPhoton Factory BL-5A21
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1micro-channel double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2micro-channel double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
211
ReflectionResolution: 2.4→50 Å / Num. all: 19643 / Num. obs: 19643 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Rsym value: 0.082 / Net I/σ(I): 38.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 1724 / Rsym value: 0.287 / % possible all: 87.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å39.51 Å
Translation3.1 Å39.51 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 907 4.6 %random
Rwork0.192 ---
obs-18828 96 %-
Solvent computationBsol: 43.931 Å2
Displacement parametersBiso mean: 28.737 Å2
Baniso -1Baniso -2Baniso -3
1--2.717 Å20 Å20 Å2
2--1.426 Å20 Å2
3---1.291 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 0 243 4189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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