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- PDB-4rev: Structure of the dirigent protein DRR206 -

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Basic information

Entry
Database: PDB / ID: 4rev
TitleStructure of the dirigent protein DRR206
ComponentsDisease resistance response protein 206
KeywordsPLANT PROTEIN / beta-barrel / stereoselective coupling / coniferyl alcohol
Function / homologyDirigent protein / Dirigent-like protein / Allene oxide cyclase/Dirigent protein / phenylpropanoid biosynthetic process / apoplast / defense response / 2,3-DIMETHYLIMIDAZOLIUM ION / Disease resistance response protein 206
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, K.-Y. / Smith, C.A. / Merkley, E.D. / Cort, J.R. / Davin, L.B. / Lewis, N.G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 angstrom Resolution with Three Isolated Active Sites.
Authors: Kim, K.W. / Smith, C.A. / Daily, M.D. / Cort, J.R. / Davin, L.B. / Lewis, N.G.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disease resistance response protein 206
B: Disease resistance response protein 206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8257
Polymers36,4732
Non-polymers3525
Water81145
1
A: Disease resistance response protein 206
hetero molecules

A: Disease resistance response protein 206
hetero molecules

A: Disease resistance response protein 206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9866
Polymers54,7103
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area8860 Å2
ΔGint-54 kcal/mol
Surface area16450 Å2
MethodPISA
2
B: Disease resistance response protein 206
hetero molecules

B: Disease resistance response protein 206
hetero molecules

B: Disease resistance response protein 206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,49015
Polymers54,7103
Non-polymers78012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8880 Å2
ΔGint-57 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.416, 88.416, 196.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-203-

CL

21B-204-

CL

31A-304-

HOH

41A-306-

HOH

51B-306-

HOH

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Components

#1: Protein Disease resistance response protein 206 / Dirigent protein PI206


Mass: 18236.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13240
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMI / 2,3-DIMETHYLIMIDAZOLIUM ION


Mass: 97.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 4% 1-butyl-2,3-dimethylimidazolium tetrafluoroborate (w/v), 0.1M Bis-Tris propane pH 7.8, and 35% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98093 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98093 Å / Relative weight: 1
ReflectionResolution: 1.95→38.5 Å / Num. all: 21935 / Num. obs: 21935 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 21.9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.001 Å / SU ML: 0.23 / σ(F): 1.83 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1134 5.18 %random
Rwork0.2029 ---
obs0.2055 21887 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→35.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 21 45 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092140
X-RAY DIFFRACTIONf_angle_d1.362890
X-RAY DIFFRACTIONf_dihedral_angle_d13.605711
X-RAY DIFFRACTIONf_chiral_restr0.06311
X-RAY DIFFRACTIONf_plane_restr0.008358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.03880.30441420.24452555X-RAY DIFFRACTION100
2.0388-2.14630.29941680.23512535X-RAY DIFFRACTION100
2.1463-2.28080.29111500.21422545X-RAY DIFFRACTION100
2.2808-2.45680.27071160.21132610X-RAY DIFFRACTION100
2.4568-2.7040.29911480.21392565X-RAY DIFFRACTION100
2.704-3.09510.22741470.20632594X-RAY DIFFRACTION100
3.0951-3.89860.20971430.19062612X-RAY DIFFRACTION100
3.8986-35.00690.27561200.19832737X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09220.62480.32162.76650.78760.7140.2122-0.2879-0.55680.7935-0.1294-0.39370.29080.16190.0890.4608-0.0441-0.08730.51820.13160.4363-32.7158-30.53682.9691
22.9262-0.29820.5245.05940.5743.70190.0698-0.4339-0.25350.6591-0.3019-0.6637-0.18510.78290.1950.28690.0001-0.10820.4328-0.01990.3965-29.0504-20.9317.6776
38.08742.6403-1.73095.1313-0.81388.49170.1255-0.07590.15750.204-0.0445-0.3680.04250.44660.00560.25470.0177-0.05590.293-0.02990.3028-33.3297-21.0345-0.6964
46.388-1.22362.7243.7827-0.14756.31850.0529-0.1617-0.49810.3689-0.0012-0.4670.13350.6982-0.02040.25080.0018-0.01920.38340.04930.3297-30.4248-25.6256-3.7368
52.4723-0.66050.81061.2804-0.05321.42890.03030.4784-0.8079-0.3271-0.1602-0.18690.20010.09140.04760.5766-0.13240.07220.3806-0.1230.418-1.192-12.563622.469
66.94472.5627-0.85094.732-2.50346.0598-0.1980.7544-0.7029-0.1287-0.134-0.03870.1789-0.80830.50230.4604-0.0866-0.06180.5359-0.19140.4407-11.4823-11.579717.1683
72.3623-0.12291.45477.571-1.18197.51310.0390.2327-0.1388-0.1916-0.00870.14340.347-0.36770.1430.3177-0.0413-0.03440.3418-0.0560.1881-8.5374-7.580624.903
83.59761.08731.63933.59961.74586.19030.07570.3779-0.6266-0.06550.09010.00660.7670.1221-0.14860.40090.0047-0.01530.3072-0.03250.2976-6.1702-12.274127.8494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 184 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 74 )
6X-RAY DIFFRACTION6chain 'B' and (resid 75 through 104 )
7X-RAY DIFFRACTION7chain 'B' and (resid 110 through 135 )
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 184 )

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