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- PDB-1vji: Gene Product of At1g76680 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 1vji
TitleGene Product of At1g76680 from Arabidopsis thaliana
Components12-oxophytodienoate reductase (OPR1)
KeywordsPLANT PROTEIN / Structural genomics / Arabidopsis Thaliana / Center for Eukaryotic Structural Genomics / Protein Structure Initiative / CESG
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / oxylipin biosynthetic process / NADPH dehydrogenase activity / fatty acid biosynthetic process / FMN binding / oxidoreductase activity / cytoplasm / 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 / 12-oxophytodienoate reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.003 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Johnson, K.A. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2005
Title: X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1.
Authors: Fox, B.G. / Malone, T.E. / Johnson, K.A. / Madson, S.E. / Aceti, D. / Bingman, C.A. / Blommel, P.G. / Buchan, B. / Burns, B. / Cao, J. / Cornilescu, C.C. / Doreleijers, J. / Ellefson, J. / ...Authors: Fox, B.G. / Malone, T.E. / Johnson, K.A. / Madson, S.E. / Aceti, D. / Bingman, C.A. / Blommel, P.G. / Buchan, B. / Burns, B. / Cao, J. / Cornilescu, C.C. / Doreleijers, J. / Ellefson, J. / Frederick, R. / Geetha, H. / Hruby, D. / Jeon, W.B. / Kimball, T. / Kunert, J. / Markley, J.L. / Newman, C. / Olson, A. / Peterson, F.C. / Phillips, G.N. / Primm, J. / Ramirez, B. / Rosenberg, N.S. / Runnels, M. / Seder, K. / Shaw, J. / Smith, D.W. / Sreenath, H. / Song, J. / Sussman, M.R. / Thao, S. / Troestler, D. / Tyler, E. / Tyler, R. / Ulrich, E. / Vinarov, D. / Vojtik, F. / Volkman, B.F. / Wesenberg, G. / Wrobel, R.L. / Zhang, J. / Zhao, Q. / Zolnai, Z.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 6, 2016Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS ARE UNCERTAIN OF THE BIOLOGICAL UNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase (OPR1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6722
Polymers41,2161
Non-polymers4561
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.688, 88.066, 149.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein 12-oxophytodienoate reductase (OPR1)


Mass: 41215.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g76680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LAH7
#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.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Methyl ether, Polyethylene glycol 5k,Calcium Chloride, MES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris1droppH8.0
3100 mM1dropNaCl
40.3 mMTCEP1drop
58.75-10 %PEG5000 MME1reservoir
60.1 MTEA1reservoirpH8.0
70.275-0.35 Mglycine1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2003 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20816 / % possible obs: 98.2 % / Rmerge(I) obs: 0.07
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2-2.050.875192
2.05-2.10.651193.6
2.1-2.150.507194.5
2.15-2.220.414196.4
2.22-2.290.349197.8
2.29-2.370.291199.2
2.37-2.470.26199.2
2.47-2.580.199199.9
2.58-2.710.1561100
2.71-2.880.108199.9
2.88-3.110.0761100
3.11-3.420.0541100
3.42-3.910.0341100
3.91-4.930.0261100
4.93-500.025199.9
Reflection
*PLUS
Lowest resolution: 43.85 Å / Num. obs: 20780 / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 92 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.816

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.1 / Cor.coef. Fo:Fc: 59 / Cor.coef. Io to Ic: 35.6
Highest resolutionLowest resolution
Translation3 Å30 Å

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Processing

Software
NameVersionClassificationNB
AMoRECCP4 4.2phasing
REFMACrefmac_5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.4data extraction
RefinementResolution: 2.003→43.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.781 / SU ML: 0.16 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.23
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1072 5.159 %RANDOM
Rwork0.2062 ---
all0.21 ---
obs-19708 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 31.114 Å2
Baniso -1Baniso -2Baniso -3
1--0.713 Å20 Å20 Å2
2--1.89 Å20 Å2
3----1.176 Å2
Refinement stepCycle: LAST / Resolution: 2.003→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 31 107 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212855
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9623881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1115349
X-RAY DIFFRACTIONr_chiral_restr0.1380.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022227
X-RAY DIFFRACTIONr_nbd_refined0.2250.21433
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.29
X-RAY DIFFRACTIONr_mcbond_it1.2191.51745
X-RAY DIFFRACTIONr_mcangle_it1.96622813
X-RAY DIFFRACTIONr_scbond_it3.04531110
X-RAY DIFFRACTIONr_scangle_it4.2184.51068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.003-2.05470.347810.27212911518
2.055-2.1110.359660.21813581517
2.111-2.17210.352870.26512971464
2.172-2.23890.3660.2513171422
2.239-2.31230.331690.23512881380
2.312-2.39340.36600.21312551323
2.393-2.48360.275690.20412261306
2.484-2.58490.35640.20911831248
2.585-2.69970.317650.22111121177
2.7-2.83130.274710.22210781150
2.831-2.98420.35520.21610491101
2.984-3.16490.283580.2179711029
3.165-3.3830.289550.224931986
3.383-3.65340.299350.199879914
3.653-4.00110.217390.171802841
4.001-4.47180.24410.165734775
4.472-5.16050.259290.164664693
5.161-6.31270.307300.197559589
6.313-8.89570.268250.202441466
8.896-74.53560.319100.237273283
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.89
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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