[English] 日本語
Yorodumi
- PDB-8kga: SlNDPS1-AtcPT4 Chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kga
TitleSlNDPS1-AtcPT4 Chimera
ComponentsDimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homology
Function and homology information


dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / polyprenyltransferase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / chloroplast stroma / protein glycosylation / response to cold ...dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / polyprenyltransferase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / chloroplast stroma / protein glycosylation / response to cold / chloroplast / magnesium ion binding
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
MALONATE ION / DI(HYDROXYETHYL)ETHER / Dimethylallylcistransferase CPT1, chloroplastic / Dehydrodolichyl diphosphate synthase 2
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.182 Å
AuthorsSuenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Yamaguchi, H. / Yanbe, F. / Waki, T. ...Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Yamaguchi, H. / Yanbe, F. / Waki, T. / Tozawa, Y. / Miyagi-Inoue, Y. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S. / Takahashi, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
Japan Society for the Promotion of Science (JSPS)22K19143 Japan
Japan Society for the Promotion of Science (JSPS)22KJ1466 Japan
Japan Society for the Promotion of Science (JSPS)20H02909 Japan
CitationJournal: To Be Published
Title: Biosynthesising various rubber-like polymers by reconstituting prenyltransferases on Hevea rubber particles: molecular and structural bases of the versatile system
Authors: Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Mikami, T. / Takahashi, T. / Minakawa, C. / Yamaguchi, H. / Yanbe, F. / Waki, T. / ...Authors: Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Mikami, T. / Takahashi, T. / Minakawa, C. / Yamaguchi, H. / Yanbe, F. / Waki, T. / Tozawa, Y. / Miyagi-Inoue, Y. / Fushihara, K. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S. / Takahashi, S.
History
DepositionAug 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
B: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4149
Polymers60,8072
Non-polymers6077
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-20 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.110, 90.107, 126.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 53 - 297 / Label seq-ID: 11 - 255

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2 / Cis-prenyltransferase 1 / SlCPT1 / Neryl-diphosphate synthase 1


Mass: 30403.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato), (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: CPT1, NDPS1, At5g58770, CPT1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C1K5M2, UniProt: Q56Y11, dimethylallylcistransferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Sodium malonate, PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 465239 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.998 / Rrim(I) all: 0.131 / Net I/σ(I): 9.74
Reflection shellResolution: 2.18→2.31 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 10711 / CC1/2: 0.576 / Rrim(I) all: 3.06 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.182→48.883 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.268 / SU ML: 0.194 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.25 1783 5.055 %
Rwork0.2033 33488 -
all0.206 --
obs-35271 99.878 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.667 Å2
Baniso -1Baniso -2Baniso -3
1-3.049 Å20 Å20 Å2
2--1.911 Å20 Å2
3----4.96 Å2
Refinement stepCycle: LAST / Resolution: 2.182→48.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 40 61 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163822
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.6425270
X-RAY DIFFRACTIONr_angle_other_deg0.4211.5748822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.427517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50210750
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.50210184
X-RAY DIFFRACTIONr_chiral_restr0.060.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_nbd_refined0.2180.2764
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23235
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.210
X-RAY DIFFRACTIONr_nbd_other0.260.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.24
X-RAY DIFFRACTIONr_mcbond_it5.266.7591904
X-RAY DIFFRACTIONr_mcbond_other5.2616.7541903
X-RAY DIFFRACTIONr_mcangle_it7.53512.0842380
X-RAY DIFFRACTIONr_mcangle_other7.53312.0882381
X-RAY DIFFRACTIONr_scbond_it6.4277.4242019
X-RAY DIFFRACTIONr_scbond_other6.4257.4252020
X-RAY DIFFRACTIONr_scangle_it9.49613.3282890
X-RAY DIFFRACTIONr_scangle_other9.49513.3282891
X-RAY DIFFRACTIONr_lrange_it11.88465.764288
X-RAY DIFFRACTIONr_lrange_other11.88365.7634289
X-RAY DIFFRACTIONr_ncsr_local_group_10.1540.056715
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.153750.05006
12AX-RAY DIFFRACTIONLocal ncs0.153750.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.182-2.2380.4231570.40123810.40225640.8560.84898.9860.396
2.238-2.30.3561280.36823520.36724830.8730.86699.87920.353
2.3-2.3660.3421210.31823240.31924460.9010.89999.95910.302
2.366-2.4390.3261100.31122600.31223720.90.9199.91570.288
2.439-2.5190.311090.27321790.27522880.9230.9371000.243
2.519-2.6070.2881270.24420750.24722030.940.95399.95460.211
2.607-2.7050.2581210.24320300.24421540.9570.95999.86070.209
2.705-2.8150.291890.2320070.23220960.9480.9651000.194
2.815-2.940.265920.21619050.21919970.9560.9681000.184
2.94-3.0830.2761050.20918110.21319160.9530.9711000.183
3.083-3.2490.288770.20617470.20918240.950.9731000.181
3.249-3.4450.251940.21416270.21617210.9640.9731000.196
3.445-3.6810.262770.19815540.20116310.9640.9791000.185
3.681-3.9740.267740.19714430.215170.9530.9761000.187
3.974-4.3510.222690.16613310.1714000.9710.9821000.168
4.351-4.860.19630.14412410.14613040.9780.9871000.156
4.86-5.6020.221550.15710810.1611360.9720.9871000.178
5.602-6.8390.245510.2069270.2089780.9670.9751000.222
6.839-9.5780.222400.177560.1727960.9680.9821000.209
9.578-48.8830.167240.2034570.2024840.9770.96799.38020.264

+
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://pdbjlc1.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