[English] 日本語
Yorodumi
- PDB-4rev: Structure of the dirigent protein DRR206 -

+
Open data


ID or keywords:

Loading...

-
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 / response to biotic stimulus / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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 / Chloride


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more