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- PDB-4qtz: Crystal Structure of Cinnamyl-Alcohol Dehydrogenase 2 -

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Basic information

Entry
Database: PDB / ID: 4qtz
TitleCrystal Structure of Cinnamyl-Alcohol Dehydrogenase 2
ComponentsDihydroflavonol-4-reductase
KeywordsOXIDOREDUCTASE / dehydrogenase / monolignol / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,3341
Polymers35,3341
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.661, 76.131, 105.717
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: 35333.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g005170 / Production host: Escherichia coli (E. coli)
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.: 281 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
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: Jan 1, 2012 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25.96 Å / Num. all: 20860 / Num. obs: 20860 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.13 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C29

2c29


Resolution: 2→25.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 117174.16 / 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
Rfree0.245 2006 9.9 %RANDOM
Rwork0.19 ---
obs0.19 20276 95.4 %-
all-20860 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3793 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--3.35 Å20 Å2
3----3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→25.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 281 2767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 324 10.7 %
Rwork0.217 2714 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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