[English] 日本語
Yorodumi
- PDB-7w8v: DMSPP- and Trp-bound 6-dimethylallyl tryptophan synthase, IptA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w8v
TitleDMSPP- and Trp-bound 6-dimethylallyl tryptophan synthase, IptA
Components6-dimethylallyltryptophan synthase
KeywordsTRANSFERASE / aromatic prenyltransferase / stpreptomyces / secondary metabolites
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / 6-dimethylallyltryptophan synthase
Function and homology information
Biological speciesStreptomyces sp. SN-593 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSuemune, H. / Nagano, S. / Tomoya, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of a 6-dimethylallyltryptophan synthase, IptA: Insights into substrate tolerance and enhancement of prenyltransferase activity.
Authors: Suemune, H. / Nishimura, D. / Mizutani, K. / Sato, Y. / Hino, T. / Takagi, H. / Shiozaki-Sato, Y. / Takahashi, S. / Nagano, S.
History
DepositionDec 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 6-dimethylallyltryptophan synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2894
Polymers39,7261
Non-polymers5623
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-8 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.686, 45.090, 78.407
Angle α, β, γ (deg.)90.000, 97.189, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein 6-dimethylallyltryptophan synthase / Tryptophan 6-prenyltransferase


Mass: 39726.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SN-593 (bacteria) / Gene: iptA, RVR_4274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6RT90
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: HPEPES pH7.5, Ammoniumu Sulfate

-
Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→49.3 Å / Num. obs: 44406 / % possible obs: 95.82 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.926 / Net I/σ(I): 7.68
Reflection shellResolution: 1.61→1.671 Å / Num. unique obs: 4317 / CC1/2: 0.569

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W8U

7w8u


Resolution: 1.61→49.3 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 2152 5.04 %
Rwork0.193 40570 -
obs0.1946 42722 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.73 Å2
Refinement stepCycle: LAST / Resolution: 1.61→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 34 312 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852674
X-RAY DIFFRACTIONf_angle_d1.0053661
X-RAY DIFFRACTIONf_chiral_restr0.06416
X-RAY DIFFRACTIONf_plane_restr0.0077481
X-RAY DIFFRACTIONf_dihedral_angle_d22.3793938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.2681380.21562701X-RAY DIFFRACTION97.33
1.65-1.690.29681300.21632742X-RAY DIFFRACTION97.62
1.69-1.740.25491510.20542741X-RAY DIFFRACTION97.41
1.74-1.790.24421160.20552784X-RAY DIFFRACTION97.87
1.79-1.850.25411420.20412726X-RAY DIFFRACTION97.12
1.85-1.910.25271300.22182741X-RAY DIFFRACTION97.09
1.91-1.990.30141520.22282688X-RAY DIFFRACTION95.91
1.99-2.080.2361570.20692711X-RAY DIFFRACTION97.29
2.08-2.190.25521530.19062642X-RAY DIFFRACTION94.68
2.19-2.330.23891420.19572570X-RAY DIFFRACTION91.1
2.33-2.510.23521600.19652623X-RAY DIFFRACTION92.83
2.51-2.760.23851390.19822617X-RAY DIFFRACTION93.01
2.76-3.160.23221700.19192641X-RAY DIFFRACTION94.11
3.16-3.980.16841380.17642809X-RAY DIFFRACTION97.68
3.98-49.30.17331340.1752834X-RAY DIFFRACTION96.33

+
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