[English] 日本語
Yorodumi
- PDB-6dxe: Crystal structure of chalcone synthase from Arabidopsis thaliana ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dxe
TitleCrystal structure of chalcone synthase from Arabidopsis thaliana - M64I F170S G173A S213G Q217A T270V C347S mutant
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


regulation of anthocyanin biosynthetic process / chalcone synthase activity / plant-type vacuole membrane / chalcone synthase / auxin polar transport / naringenin-chalcone synthase activity / response to jasmonic acid / flavonoid biosynthetic process / response to auxin / response to gravity ...regulation of anthocyanin biosynthetic process / chalcone synthase activity / plant-type vacuole membrane / chalcone synthase / auxin polar transport / naringenin-chalcone synthase activity / response to jasmonic acid / flavonoid biosynthetic process / response to auxin / response to gravity / response to UV-B / response to wounding / response to oxidative stress / endoplasmic reticulum / nucleus
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.608 Å
AuthorsLiou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1709616 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.
Authors: Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chalcone synthase
C: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,0352
Polymers86,0352
Non-polymers00
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-17 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 55.900, 100.210
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Chalcone synthase / / Naringenin-chalcone synthase / Protein TRANSPARENT TESTA 4


Mass: 43017.441 Da / Num. of mol.: 2 / Mutation: M64I, F170S, G173A, S213G, Q217A, T270V, C347S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHS, TT4, At5g13930, MAC12.11, MAC12.14 / Plasmid: pHis8-4B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13114, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.125 NaSCN, 20% (v/v) PEG 3350, and 5 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2018
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.608→60.11 Å / Num. obs: 175827 / % possible obs: 91.6 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04526 / Rpim(I) all: 0.03089 / Rrim(I) all: 0.05506 / Net I/σ(I): 11.1
Reflection shellResolution: 1.608→1.665 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5779 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 7995 / CC1/2: 0.778 / Rpim(I) all: 0.392 / Rrim(I) all: 0.7013 / % possible all: 76.72

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.608→60.107 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2015 3515 2 %
Rwork0.1698 --
obs0.1704 175827 85.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.54 Å2 / Biso mean: 21.36 Å2 / Biso min: 7.13 Å2
Refinement stepCycle: final / Resolution: 1.608→60.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 0 859 6815
Biso mean---31.6 -
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016188
X-RAY DIFFRACTIONf_angle_d1.2588395
X-RAY DIFFRACTIONf_chiral_restr0.051959
X-RAY DIFFRACTIONf_plane_restr0.0061088
X-RAY DIFFRACTIONf_dihedral_angle_d13.892313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.608-1.630.24531100.2645728583872
1.63-1.65330.28711250.26095894601973
1.6533-1.6780.31511150.25355932604774
1.678-1.70420.25081570.24796110626776
1.7042-1.73220.26671160.24016297641377
1.7322-1.7620.25011450.23556153629878
1.762-1.79410.24721150.2326476659180
1.7941-1.82860.25691550.2346681683683
1.8286-1.86590.29641340.22876770690484
1.8659-1.90650.2361430.22576876701986
1.9065-1.95090.25231180.216603672182
1.9509-1.99960.21071580.19777308746691
1.9996-2.05370.22841540.1917408756292
2.0537-2.11410.2381400.17747390753092
2.1141-2.18240.22381410.16967344748591
2.1824-2.26040.19791350.15957368750391
2.2604-2.35090.18811460.15417292743891
2.3509-2.45790.21441360.1517279741591
2.4579-2.58750.15551560.14857295745190
2.5875-2.74960.17361560.15966785694185
2.7496-2.96190.20191450.15867455760092
2.9619-3.25990.17171680.15677546771494
3.2599-3.73160.15381510.14357518766994
3.7316-4.70110.19781540.13077407756192
4.7011-60.14890.1661420.14147397753992
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)
10.59360.3158-0.09420.79520.03031.24450.0091-0.25070.10420.1323-0.10120.1259-0.16190.01420.06220.0990.00940.03020.1324-0.06010.1391-9.71395.891130.5391
24.7072-0.4858-0.7754.8173-3.64026.00680.02830.25250.2527-0.3138-0.08020.4234-0.0114-0.2557-0.0270.21760.0733-0.08070.1387-0.03380.2385-25.378812.1274.2055
31.37250.5141-1.00740.6629-0.68871.5922-0.05570.05630.4594-0.0130.08440.2229-0.2711-0.1578-0.0390.21660.0632-0.04580.1361-0.03760.2852-16.870919.403214.8642
40.66440.5612-0.95941.8967-2.85766.17910.0935-0.1410.35460.18510.01020.2112-0.465-0.2119-0.03950.1780.0260.00420.1378-0.08120.1847-8.300816.42830.0724
50.48690.1629-0.72640.7954-0.39381.33370.0522-0.30740.19170.0864-0.1380.0312-0.22940.14030.01290.1458-0.00650.00440.1967-0.07090.1240.101212.965635.6572
60.85640.04580.00030.5646-0.09450.5210.0377-0.0770.0786-0.0447-0.09210.0668-0.02380.00290.0520.11470.02990.00880.0988-0.02870.1041-6.47035.804125.0471
70.76110.30370.8971.68931.37925.16450.091-0.407-0.01730.2634-0.18180.10230.2699-0.0740.11460.1436-0.01990.02160.21040.00680.1147-7.0445-5.084740.9113
81.67772.6682-0.18964.3994-0.22360.0343-0.20130.230.0642-0.65440.15090.14050.15960.00430.01440.24610.0295-0.01650.1384-0.0010.1093-5.38682.38668.6518
91.55840.1804-0.03052.5925-1.21253.71730.0089-0.0069-0.2642-0.1472-0.0529-0.0020.5375-0.02830.02680.1794-0.0043-0.00690.0867-0.01270.1338-13.2938-14.484923.8254
101.9874-0.8206-0.40297.63241.57983.5897-0.0111-0.0695-0.1973-0.0532-0.01380.51740.2326-0.28430.020.09360.0222-0.01580.1253-0.01790.1665-22.7319-5.422122.44
112.12770.4956-0.97532.3238-0.92813.28290.0477-0.20460.00120.1025-0.09010.20690.0981-0.21130.03980.0856-0.0195-0.010.1271-0.03790.095-15.8841-5.232932.4006
120.6524-0.06380.33520.668-0.1570.7806-0.001-0.1541-0.1449-0.0353-0.2618-0.2760.04380.42470.2260.11620.05780.00460.21080.03940.099417.11891.8823.2665
131.17810.3392-0.25422.5776-1.68121.1051-0.36710.07770.39490.4249-0.3036-0.3457-0.68850.72110.51210.3023-0.1339-0.11450.34570.09540.249526.410730.480211.0331
141.00850.10440.19411.4836-0.77731.0893-0.10910.04370.006-0.1671-0.0231-0.071-0.02080.28160.10920.14530.03340.02870.21660.03740.096717.213310.12719.6422
151.7701-0.14770.32141.05170.32070.75360.01130.0475-0.2055-0.1547-0.107-0.09120.18380.15510.05380.14690.06840.040.1340.02430.11217.7913-5.228417.9111
161.01790.3753-0.13670.6318-0.3581.24960.0249-0.19840.03420.0578-0.1472-0.0887-0.08440.26920.09520.09330.01890.00310.19770.02330.090713.61617.94825.529
173.2854-2.98932.91748.4948-7.51319.3328-0.1381-0.75030.3410.41720.1265-0.0337-0.41470.0222-0.00680.1732-0.0588-0.01210.4266-0.09050.206319.834914.315443.2422
181.1856-0.36081.38990.2125-0.16862.4892-0.0301-0.31220.20170.1883-0.0871-0.1331-0.34550.57790.16390.1631-0.0682-0.03090.44980.03220.191128.369913.258137.8438
192.4427-2.1304-0.46893.8701-0.67041.15590.0206-0.12440.09130.0817-0.0781-0.3067-0.05110.45020.02210.0854-0.0010.00220.36490.06470.146829.67536.262626.3413
201.5065-0.19620.63410.4166-0.25820.77430.067-0.4534-0.0660.1188-0.1051-0.0676-0.15240.49780.06240.02550.0524-0.02260.4820.11330.157324.38843.207236.6216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 48 )A7 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 67 )A49 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 95 )A68 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 122 )A96 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 159 )A123 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 230 )A160 - 230
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 252 )A231 - 252
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 276 )A253 - 276
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 312 )A277 - 312
10X-RAY DIFFRACTION10chain 'A' and (resid 313 through 343 )A313 - 343
11X-RAY DIFFRACTION11chain 'A' and (resid 344 through 395 )A344 - 395
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 48 )C7 - 48
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 66 )C49 - 66
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 122 )C67 - 122
15X-RAY DIFFRACTION15chain 'C' and (resid 123 through 159 )C123 - 159
16X-RAY DIFFRACTION16chain 'C' and (resid 160 through 276 )C160 - 276
17X-RAY DIFFRACTION17chain 'C' and (resid 277 through 296 )C277 - 296
18X-RAY DIFFRACTION18chain 'C' and (resid 297 through 326 )C297 - 326
19X-RAY DIFFRACTION19chain 'C' and (resid 327 through 362 )C327 - 362
20X-RAY DIFFRACTION20chain 'C' and (resid 363 through 395 )C363 - 395

+
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