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- PDB-4quk: Crystal Structure of Cinnamyl-Alcohol Dehydrogenase 2 Mutant K169A -

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Basic information

Entry
Database: PDB / ID: 4quk
TitleCrystal Structure of Cinnamyl-Alcohol Dehydrogenase 2 Mutant K169A
ComponentsDihydroflavonol-4-reductase
KeywordsOXIDOREDUCTASE / dehydrogenase / monolignol / mutant / short-chain dehydrogenase/reductase / Rossmann fold
Function / homology
Function and homology information


cinnamoyl-CoA reductase / cinnamyl-alcohol dehydrogenase activity / phenylpropanoid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / cytoplasm
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cinnamoyl-CoA reductase CAD2
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsPan, H. / Wang, X.
CitationJournal: Plant Cell / Year: 2014
Title: Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis.
Authors: Pan, H. / Zhou, R. / Louie, G.V. / Muhlemann, J.K. / Bomati, E.K. / Bowman, M.E. / Dudareva, N. / Dixon, R.A. / Noel, J.P. / Wang, X.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroflavonol-4-reductase


Theoretical massNumber of molelcules
Total (without water)35,1051
Polymers35,1051
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.797, 76.565, 106.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydroflavonol-4-reductase / Cinnamyl alcohol dehydrogenase 2


Mass: 35105.203 Da / Num. of mol.: 1 / Mutation: K169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g005170 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G7IYC1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→28.56 Å / Num. all: 24741 / Num. obs: 24741 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 42.2
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 10.2 / % possible all: 88.7

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4QTZ

4qtz


Resolution: 1.9→28.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 221965.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2433 9.9 %RANDOM
Rwork0.185 ---
obs0.185 24520 98 %-
all-24741 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.291 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--1.36 Å20 Å2
3----0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 359 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 351 9.5 %
Rwork0.189 3340 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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