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- PDB-5vkt: Cinnamyl alcohol dehydrogenases (SbCAD4) from Sorghum bicolor (L.... -

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Basic information

Entry
Database: PDB / ID: 5vkt
TitleCinnamyl alcohol dehydrogenases (SbCAD4) from Sorghum bicolor (L.) Moench
ComponentsCinnamyl alcohol dehydrogenases (SbCAD4)
KeywordsOXIDOREDUCTASE / Cinnamyl alcohol dehydrogenases / CAD / sinapyl alchohl dehydrogenase / SAD / Sorghum / Dehydrogenase / NADP+ / NADPH / p-coumaraldehyde / coniferaldehyde / sinapaldehyde
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / D-MALATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PKS_ER domain-containing protein
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.827 Å
AuthorsWalker, A.M. / Jun, S.Y. / Kang, C.
CitationJournal: Plant Physiol. / Year: 2017
Title: The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD4.
Authors: Jun, S.Y. / Walker, A.M. / Kim, H. / Ralph, J. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionApr 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cinnamyl alcohol dehydrogenases (SbCAD4)
B: Cinnamyl alcohol dehydrogenases (SbCAD4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,19311
Polymers75,8562
Non-polymers1,3369
Water15,925884
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cinnamyl alcohol dehydrogenases (SbCAD4)
hetero molecules

B: Cinnamyl alcohol dehydrogenases (SbCAD4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,19311
Polymers75,8562
Non-polymers1,3369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4900 Å2
ΔGint-64 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.597, 74.280, 97.288
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cinnamyl alcohol dehydrogenases (SbCAD4)


Mass: 37928.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_002G195400 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: C5XC49, cinnamyl-alcohol dehydrogenase

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Non-polymers , 7 types, 893 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole pH 7.0, 8% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.827→45.683 Å / Num. obs: 67962 / % possible obs: 97.4 % / Redundancy: 1.8 % / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
HKL-3000phasing
RefinementResolution: 1.827→45.683 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74
RfactorNum. reflection% reflection
Rfree0.1866 2000 2.94 %
Rwork0.1632 --
obs0.1639 67935 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.827→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5178 0 74 884 6136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035434
X-RAY DIFFRACTIONf_angle_d0.5687381
X-RAY DIFFRACTIONf_dihedral_angle_d9.8373159
X-RAY DIFFRACTIONf_chiral_restr0.046850
X-RAY DIFFRACTIONf_plane_restr0.003956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8271-1.87280.32321080.27623547X-RAY DIFFRACTION74
1.8728-1.92340.27291330.25274412X-RAY DIFFRACTION92
1.9234-1.980.26741440.21844730X-RAY DIFFRACTION98
1.98-2.0440.22731450.19514779X-RAY DIFFRACTION100
2.044-2.1170.20581470.18094832X-RAY DIFFRACTION100
2.117-2.20180.19131450.16834812X-RAY DIFFRACTION100
2.2018-2.3020.19351470.16544816X-RAY DIFFRACTION100
2.302-2.42330.1921460.1594836X-RAY DIFFRACTION100
2.4233-2.57510.19291460.1614838X-RAY DIFFRACTION100
2.5751-2.77390.20861470.15784830X-RAY DIFFRACTION100
2.7739-3.0530.16551470.15514818X-RAY DIFFRACTION100
3.053-3.49470.18081470.15224863X-RAY DIFFRACTION100
3.4947-4.40240.14221480.13314863X-RAY DIFFRACTION100
4.4024-45.69710.15731500.14754959X-RAY DIFFRACTION100

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