[English] 日本語
Yorodumi
- PDB-5ynt: Crystal structure of an aromatic prenyltransferase FAMD1 from Fis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ynt
TitleCrystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyhapalindole G dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / DIMETHYLALLYL DIPHOSPHATE / IMIDAZOLE / Hapalindole dimethylallyltransferase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.79 Å
AuthorsWang, J. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis.
Authors: Wang, J. / Chen, C.C. / Yang, Y. / Liu, W. / Ko, T.P. / Shang, N. / Hu, X. / Xie, Y. / Huang, J.W. / Zhang, Y. / Guo, R.T.
History
DepositionOct 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7698
Polymers73,9782
Non-polymers7926
Water12,971720
1
A: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3964
Polymers36,9891
Non-polymers4073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3734
Polymers36,9891
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.398, 211.400, 82.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-720-

HOH

21A-772-

HOH

31B-715-

HOH

41B-741-

HOH

51B-861-

HOH

61B-862-

HOH

-
Components

#1: Protein aromatic prenyltransferase


Mass: 36988.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: ambP3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V5TDY7
#2: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 2.94 Å3/Da / Density % sol: 58.15 % / Mosaicity: 0.249 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 8, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→25 Å / Num. obs: 76749 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.024 / Rrim(I) all: 0.051 / Χ2: 0.581 / Net I/σ(I): 10.7 / Num. measured all: 332166
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.854.30.25575280.9540.1390.2910.43899.3
1.85-1.934.30.20375950.9650.110.2320.491100
1.93-2.024.40.13976360.9850.0750.1580.494100
2.02-2.124.40.10176070.9890.0540.1150.545100
2.12-2.254.40.07576440.9950.040.0850.539100
2.25-2.434.40.0676480.9970.0320.0680.548100
2.43-2.674.40.04876630.9980.0260.0540.586100
2.67-3.064.40.03676890.9990.0190.0410.64899.9
3.06-3.854.30.03777460.9970.020.0420.99499.9
3.85-254.20.02379930.9990.0130.0260.52199.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.79→25 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.103 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17062 3876 5.1 %RANDOM
Rwork0.10889 ---
obs0.11192 72853 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å2-0 Å2
2---0.36 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.79→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 49 720 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195103
X-RAY DIFFRACTIONr_bond_other_d00.024612
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9496936
X-RAY DIFFRACTIONr_angle_other_deg0.778310718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55924.659249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65115807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5061520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215685
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021073
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2242.0132457
X-RAY DIFFRACTIONr_mcbond_other5.1872.0122456
X-RAY DIFFRACTIONr_mcangle_it5.95233067
X-RAY DIFFRACTIONr_mcangle_other5.9643.0013068
X-RAY DIFFRACTIONr_scbond_it6.6922.4952646
X-RAY DIFFRACTIONr_scbond_other6.6922.4952646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1043.5313868
X-RAY DIFFRACTIONr_long_range_B_refined7.12940.60922554
X-RAY DIFFRACTIONr_long_range_B_other6.8339.46721781
X-RAY DIFFRACTIONr_rigid_bond_restr5.75239715
X-RAY DIFFRACTIONr_sphericity_free39.8835129
X-RAY DIFFRACTIONr_sphericity_bonded17.385510161
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 293 -
Rwork0.149 5183 -
obs--97.7 %

+
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