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- PDB-5dxx: Crystal structure of Dbr2 -

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Basic information

Entry
Database: PDB / ID: 5dxx
TitleCrystal structure of Dbr2
ComponentsArtemisinic aldehyde Delta(11(13)) reductase
KeywordsOXIDOREDUCTASE / Dbr2
Function / homology
Function and homology information


artemisinic aldehyde Delta11(13)-reductase / 12-oxophytodienoate reductase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Artemisinic aldehyde Delta(11(13)) reductase
Similarity search - Component
Biological speciesArtemisia annua (sweet wormwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, L. / Chen, T.T. / Xu, Y.C.
CitationJournal: to be published
Title: The Crystal structure of Dbr2
Authors: Li, L.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Artemisinic aldehyde Delta(11(13)) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9522
Polymers42,4961
Non-polymers4561
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.580, 80.970, 86.160
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 Artemisinic aldehyde Delta(11(13)) reductase / Dbr2


Mass: 42496.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: DBR2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(DE3) RIPL
References: UniProt: C5H429, artemisinic aldehyde Delta11(13)-reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris, 25% PEG3350 / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→38.04 Å / Num. obs: 65791 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.97 % / Biso Wilson estimate: 11.78 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.05 / Χ2: 0.986 / Net I/σ(I): 26.54 / Num. measured all: 458761
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.490.9660.2296.9924404484148150.25599.5
1.49-1.530.9820.1929.8131442469746970.208100
1.53-1.570.9890.16311.8732911453845380.176100
1.57-1.620.9920.13813.6832378445844570.149100
1.62-1.670.9940.11815.7131201428342830.127100
1.67-1.730.9950.09918.1830525419441940.106100
1.73-1.80.9970.08121.329558405440540.087100
1.8-1.870.9970.06924.2328406389238920.074100
1.87-1.960.9980.05827.8327053370537050.063100
1.96-2.050.9980.0532.1626184358535840.054100
2.05-2.160.9980.04535.5824725339833980.048100
2.16-2.290.9990.04138.6423443323332320.045100
2.29-2.450.9990.0440.1921823302530240.043100
2.45-2.650.9990.0442.0320312284528430.04399.9
2.65-2.90.9990.03844.9118663263926370.04199.9
2.9-3.240.9990.03747.116558238423810.0499.9
3.24-3.740.9990.03648.614293212921250.03999.8
3.74-4.590.9980.03549.1911858181618040.03899.3
4.59-6.480.9990.03348.449166143314180.03699
6.480.9970.03443.3638588627100.03882.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.1phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.45→38.032 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 1967 3 %
Rwork0.1298 63602 -
obs0.1308 65569 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.08 Å2 / Biso mean: 17.3848 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: final / Resolution: 1.45→38.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 31 437 3373
Biso mean--19.31 30.22 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063047
X-RAY DIFFRACTIONf_angle_d0.9954153
X-RAY DIFFRACTIONf_chiral_restr0.039455
X-RAY DIFFRACTIONf_plane_restr0.005537
X-RAY DIFFRACTIONf_dihedral_angle_d13.0661110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48620.18261390.11974496463599
1.4862-1.52640.18991390.106344924631100
1.5264-1.57130.16461390.102444884627100
1.5713-1.6220.16291410.101345424683100
1.622-1.680.14851390.103445124651100
1.68-1.74730.16771400.105345314671100
1.7473-1.82680.1551400.110845214661100
1.8268-1.92310.15671400.113545284668100
1.9231-2.04360.16661410.119545494690100
2.0436-2.20140.1491410.123545634704100
2.2014-2.42290.17041410.132845704711100
2.4229-2.77340.17661430.144945984741100
2.7734-3.49380.17061420.147846224764100
3.4938-38.04510.15281420.1464590473295

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