[English] 日本語
Yorodumi
- PDB-9kaj: Crystal Structure of Chalcone Syntase from Physcomitrella patens ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kaj
TitleCrystal Structure of Chalcone Syntase from Physcomitrella patens complexed with Coenzyme A
ComponentsChalcone synthase
KeywordsTRANSFERASE / Flavonoid / chalcone synthase
Function / homology
Function and homology information


chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
COENZYME A / Chalcone synthase
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsImaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Society for the Promotion of Science (JSPS)21H02115 Japan
Japan Society for the Promotion of Science (JSPS)24K23286 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: To Be Published
Title: Structural basis, dynamics, and mode of action of enhancer of flavonoid production in metabolon
Authors: Imaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chalcone synthase
B: Chalcone synthase
C: Chalcone synthase
D: Chalcone synthase
E: Chalcone synthase
F: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,64513
Polymers268,0946
Non-polymers2,5517
Water5,819323
1
A: Chalcone synthase
D: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3186
Polymers89,3652
Non-polymers9544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Chalcone synthase
hetero molecules

B: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1944
Polymers89,3652
Non-polymers8302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
3
C: Chalcone synthase
E: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1323
Polymers89,3652
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.170, 198.990, 68.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 97 or resid 99...
d_2ens_1(chain "B" and (resid 14 through 97 or resid 99...
d_3ens_1(chain "C" and (resid 14 through 97 or resid 99...
d_4ens_1(chain "D" and (resid 14 through 97 or resid 99...
d_5ens_1(chain "E" and (resid 14 through 97 or resid 99...
d_6ens_1(chain "F" and (resid 14 through 97 or resid 99...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGLEULEUAA14 - 9730 - 113
d_12VALVALARGARGAA99 - 100115 - 116
d_13ASPASPGLUGLUAA102 - 209118 - 225
d_14HISHISGLYGLYAA211 - 262227 - 278
d_15LEULEUILEILEAA264 - 270280 - 286
d_16HISHISLEULEUAA272 - 273288 - 289
d_17LYSLYSSERSERAA275 - 396291 - 412
d_21ARGARGLEULEUBB14 - 9730 - 113
d_22VALVALARGARGBB99 - 100115 - 116
d_23ASPASPGLUGLUBB102 - 209118 - 225
d_24HISHISGLYGLYBB211 - 262227 - 278
d_25LEULEUILEILEBB264 - 270280 - 286
d_26HISHISLEULEUBB272 - 273288 - 289
d_27LYSLYSSERSERBB275 - 396291 - 412
d_31ARGARGLEULEUCC14 - 9730 - 113
d_32VALVALARGARGCC99 - 100115 - 116
d_33ASPASPGLUGLUCC102 - 209118 - 225
d_34HISHISGLYGLYCC211 - 262227 - 278
d_35LEULEUILEILECC264 - 270280 - 286
d_36HISHISLEULEUCC272 - 273288 - 289
d_37LYSLYSSERSERCC275 - 396291 - 412
d_41ARGARGLEULEUDD14 - 9730 - 113
d_42VALVALARGARGDD99 - 100115 - 116
d_43ASPASPGLUGLUDD102 - 209118 - 225
d_44HISHISGLYGLYDD211 - 262227 - 278
d_45LEULEUILEILEDD264 - 270280 - 286
d_46HISHISLEULEUDD272 - 273288 - 289
d_47LYSLYSSERSERDD275 - 396291 - 412
d_51ARGARGLEULEUEE14 - 9730 - 113
d_52VALVALARGARGEE99 - 100115 - 116
d_53ASPASPGLUGLUEE102 - 209118 - 225
d_54HISHISGLYGLYEE211 - 262227 - 278
d_55LEULEUILEILEEE264 - 270280 - 286
d_56HISHISLEULEUEE272 - 273288 - 289
d_57LYSLYSSERSEREE275 - 396291 - 412
d_61ARGARGLEULEUFF14 - 9730 - 113
d_62VALVALARGARGFF99 - 100115 - 116
d_63ASPASPGLUGLUFF102 - 209118 - 225
d_64HISHISGLYGLYFF211 - 262227 - 278
d_65LEULEUILEILEFF264 - 270280 - 286
d_66HISHISLEULEUFF272 - 273288 - 289
d_67LYSLYSSERSERFF275 - 396291 - 412

NCS oper:
IDCodeMatrixVector
1given(-0.469888181673, -0.880665798482, 0.0602731126466), (0.882171860321, -0.466078360863, 0.0674074950875), (-0.0312714819385, 0.0848452292086, 0.995903299271)-54.82855576, 68.6044034468, 20.9230215372
2given(-0.537662114524, 0.843051491771, -0.013551119059), (-0.843114076832, -0.537731596361, -0.00183949012457), (-0.00883764977766, 0.0104361150854, 0.999906487352)-87.5294143482, -13.6973739203, -21.0392263985
3given(-0.272974674911, -0.639671771139, 0.718543563095), (-0.628872433718, -0.446576390613, -0.636466015948), (0.728013934596, -0.625611343051, -0.280367898446)4.16738990671, 15.0249224658, 9.07767404965
4given(-0.385550397048, -0.035786548248, -0.921992523994), (0.574248512139, 0.772831110881, -0.270130931884), (0.722211560169, -0.633601923149, -0.277414969565)-76.6566386069, -25.0987205092, -11.5105416991
5given(0.728353475708, 0.653039336668, 0.207462862189), (0.0912764238184, -0.392548501907, 0.915190847914), (0.67909486, -0.647645966879, -0.345521161012)-69.3310238836, 65.6370523646, -36.9777192321

-
Components

#1: Protein
Chalcone synthase


Mass: 44682.320 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_029015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2VAZ3, chalcone synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 76561 / % possible obs: 99 % / Redundancy: 11.7 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.968 / Rrim(I) all: 0.39 / Net I/σ(I): 7.82
Reflection shellResolution: 2.64→2.8 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 12150 / CC1/2: 0.535 / Rrim(I) all: 1.8 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.13 Å / SU ML: 0.3492 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.6586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241 3827 5 %
Rwork0.1948 72649 -
obs0.1971 76476 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.05 Å2
Refinement stepCycle: LAST / Resolution: 2.64→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17438 0 160 323 17921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012118105
X-RAY DIFFRACTIONf_angle_d1.345124524
X-RAY DIFFRACTIONf_chiral_restr0.06312713
X-RAY DIFFRACTIONf_plane_restr0.01423174
X-RAY DIFFRACTIONf_dihedral_angle_d15.60336833
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.565729156757
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.625717310195
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.915105543605
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.962622610718
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.933804680556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.670.3561380.2842612X-RAY DIFFRACTION98.14
2.67-2.710.30641380.27022618X-RAY DIFFRACTION98.57
2.71-2.750.32711410.26532678X-RAY DIFFRACTION98.39
2.75-2.780.30881380.26012599X-RAY DIFFRACTION98.31
2.78-2.830.31051390.2552655X-RAY DIFFRACTION98.66
2.83-2.870.30711410.25712666X-RAY DIFFRACTION98.66
2.87-2.920.32921390.24852643X-RAY DIFFRACTION98.93
2.92-2.970.31761420.24632693X-RAY DIFFRACTION98.92
2.97-3.020.29121380.24922614X-RAY DIFFRACTION98.46
3.02-3.080.30311400.24052674X-RAY DIFFRACTION99.05
3.08-3.140.29491410.24252675X-RAY DIFFRACTION99.26
3.14-3.210.26691410.23342673X-RAY DIFFRACTION99.29
3.21-3.290.28331410.22062676X-RAY DIFFRACTION99.33
3.29-3.370.26621410.22562682X-RAY DIFFRACTION99.23
3.37-3.460.28951420.21052691X-RAY DIFFRACTION99.19
3.46-3.560.27541410.20262678X-RAY DIFFRACTION99.47
3.56-3.680.22691410.18252690X-RAY DIFFRACTION99.93
3.68-3.810.24071450.17322741X-RAY DIFFRACTION99.79
3.81-3.960.21441410.17092689X-RAY DIFFRACTION99.86
3.96-4.140.19921430.15722715X-RAY DIFFRACTION99.65
4.14-4.360.18171430.15182707X-RAY DIFFRACTION99.58
4.36-4.630.19571430.15192723X-RAY DIFFRACTION99.34
4.63-4.990.19181440.15622731X-RAY DIFFRACTION99.14
4.99-5.490.18161450.16882741X-RAY DIFFRACTION99.45
5.49-6.280.20411450.18182762X-RAY DIFFRACTION99.32
6.28-7.910.21951470.16462786X-RAY DIFFRACTION99.26
7.91-48.130.17811490.15372837X-RAY DIFFRACTION95.64

+
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