[English] 日本語
Yorodumi
- PDB-4uj0: Crystal structure of the tomato defensin TPP3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uj0
TitleCrystal structure of the tomato defensin TPP3
ComponentsFLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN
KeywordsANTIBIOTIC / IMMUNE SYSTEM / ANTIMICROBIAL PEPTIDE / PHOSPHOLIPID / PIP2
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Flower-specific gamma-thionin-like protein/acidic protein
Similarity search - Component
Biological speciesSOLANUM LYCOPERSICUM (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRichter, V. / Lay, F.T. / Hulett, M.D. / Kvansakul, M.
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: The Tomato Defensin Tpp3 Binds Phosphatidylinositol (4,5)-Bisphosphate Via a Conserved Dimeric Cationic Grip Conformation to Mediate Cell Lysis.
Authors: Baxter, A.A. / Richter, V. / Lay, F.T. / Poon, I.K.H. / Adda, C.G. / Veneer, P.K. / Phan, T.K. / Bleackley, M.R. / Anderson, M.A. / Kvansakul, M. / Hulett, M.D.
History
DepositionApr 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN
B: FLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0883
Polymers11,0292
Non-polymers591
Water1,15364
1
A: FLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5742
Polymers5,5151
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,5151
Polymers5,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.967, 64.967, 82.398
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

-
Components

#1: Protein/peptide FLOWER-SPECIFIC GAMMA-THIONIN-LIKE PROTEIN/ACIDIC PROTEIN / TPP3


Mass: 5514.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM LYCOPERSICUM (tomato) / Fragment: RESIDUES 25-73 / Plasmid: PPIC9 / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: Q40128
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.1
Details: 0.16 M AMMONIUM ACETATE, 24% (W/V) PEG 4000, 0.1 M SODIUM CITRATE AT PH 5.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→46.46 Å / Num. obs: 11889 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 34.7 % / Biso Wilson estimate: 20.83 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 51.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 38.1 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 5.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CQK

4cqk


Resolution: 1.7→33.24 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 560 4.7 %
Rwork0.1866 --
obs0.1876 11848 99.99 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.109 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.2929 Å20 Å20 Å2
2--3.2929 Å20 Å2
3----6.5858 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 4 64 805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009786
X-RAY DIFFRACTIONf_angle_d1.11038
X-RAY DIFFRACTIONf_dihedral_angle_d14.521311
X-RAY DIFFRACTIONf_chiral_restr0.064108
X-RAY DIFFRACTIONf_plane_restr0.006134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.87110.25871330.2342746X-RAY DIFFRACTION100
1.8711-2.14180.1961400.18652758X-RAY DIFFRACTION100
2.1418-2.69830.23511410.17892803X-RAY DIFFRACTION100
2.6983-33.24650.19131460.18252981X-RAY DIFFRACTION100
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)
13.55441.2556-4.44765.1986-3.15557.50360.33890.2341-0.0698-0.2398-0.2126-0.5536-1.1425-0.112-0.5220.2484-0.03160.03990.21890.00440.21220.183320.4942-4.7242
25.71911.456-2.0775.85480.92991.9937-0.1143-0.30390.25270.25460.2874-0.1192-0.24160.50890.02790.1501-0.06310.01280.1617-0.04340.1142-3.267318.076610.2696
36.352-4.5190.96874.13742.11638.6729-0.5193-1.09570.5690.37170.3101-0.3693-0.031.55030.04860.14280.0516-0.01540.45790.01430.23344.26116.00548.6337
45.2656-2.3496-3.77926.00522.9983.229-0.3078-0.6118-0.74960.09520.0236-0.17440.86870.29850.37280.20570.03620.05620.16390.01240.19970.701810.69763.8186
52.2875-2.5313-4.12519.51574.68669.19270.3583-0.31240.28760.3460.0254-0.323-0.35370.3497-0.3650.1608-0.0230.04520.1461-0.02790.1731.675919.58662.7559
62.00023.13290.7093.86772.4999.7582-0.30781.34871.4642-2.5574-0.435-0.0584-1.8569-0.28180.55750.81740.09640.03910.2682-0.00610.4499-4.11328.33879.0793
76.39361.1365-3.03147.5872-0.791.56010.21290.69260.1927-0.218-0.08220.0925-0.0778-0.7382-0.00090.11280.043-0.0020.22020.010.1182-0.449518.9291-0.9833
83.55651.8463-0.84271.62590.67812.06380.7061-0.6864-0.0950.5664-0.3117-0.031-0.2761-0.1823-0.17640.24420.0161-0.03530.25610.03850.153-7.145118.2789-5.5982
93.93733.08090.31873.8560.60973.0745-0.2336-0.4102-0.50920.4819-0.7407-1.1873-0.70011.34620.72990.2286-0.0350.02280.27670.03950.2219-0.403128.1138-11.7863
102.0002-6.844-3.30544.85372.63921.56880.17460.31281.1167-0.64510.1371-0.7041-1.17310.0448-0.15350.68670.00280.09890.19820.00940.2627-2.96634.7673-16.2119
112.0001-2.6616-6.86265.5777-1.72436.60860.45981.0608-0.0179-0.869-0.29781.0452-0.3569-0.84090.29730.36980.1237-0.12230.2257-0.08590.3949-10.905537.6874-12.4767
128.72921.04685.07373.97883.28334.8055-1.059-0.71260.9549-0.07810.40630.6384-1.1914-0.9750.33540.33190.1047-0.0680.2122-0.01620.2809-12.035131.7334-16.1031
136.4461-0.7293-4.02092.0004-2.52333.1425-0.25790.9335-0.0752-0.620.16271.5002-0.3455-0.3549-0.08420.31810.0419-0.01320.20140.00440.171-8.524128.8298-19.0226
144.1542.66911.93734.1707-2.57297.4704-0.02820.9915-0.1639-0.16710.246-0.38720.0358-0.3002-0.15130.2350.04130.0930.2698-0.03330.1922-3.72224.2306-20.362
156.8169-1.23010.91249.09021.59153.1542-0.4029-0.3512-0.2983-0.3260.04270.7481-0.1311-0.6960.46530.1361-0.0050.0410.1296-0.05270.1835-7.511422.0887-15.1143
162.00025.25894.00612.76091.52658.1497-0.1353-0.85230.80830.2577-0.64020.8657-1.0107-1.0949-0.75660.37590.10160.12040.214-0.09730.2075-11.906331.7707-7.7873
177.6437-0.4294-3.28827.40562.51622.1507-0.0161-1.48670.24430.32820.5019-0.28610.32710.2774-0.21920.2697-0.0065-0.02330.4222-0.06730.2579-8.141935.9881-4.3794
186.97234.695-2.85364.0345-4.32338.73440.0593-0.0868-0.21640.0964-0.1407-0.41660.1740.10860.05380.11330.0285-0.00790.1582-0.01710.1144-5.944721.7391-10.46
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:19)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 20:24)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 25:30)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 31:37)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 38:41)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 42:49)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 3:6)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 7:10)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 11:14)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 15:18)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 19:22)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 23:26)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 27:30)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 31:34)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 35:38)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 39:42)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 43:49)

+
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