[English] 日本語
Yorodumi
- PDB-3i4z: Crystal structure of the dimethylallyl tryptophan synthase FgaPT2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i4z
TitleCrystal structure of the dimethylallyl tryptophan synthase FgaPT2 from Aspergillus fumigatus
ComponentsTryptophan dimethylallyltransferase
KeywordsTRANSFERASE / prenyl transferase / PT barrel / Alkaloid metabolism
Function / homology
Function and homology information


4-dimethylallyltryptophan synthase / tryptophan dimethylallyltransferase activity / fumigaclavine C biosynthetic process / prenyltransferase activity
Similarity search - Function
Tryptophan dimethylallyltransferase / Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
1,3-BUTANEDIOL / Tryptophan dimethylallyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsSchall, C. / Zocher, G. / Stehle, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria
Authors: Metzger, U. / Schall, C. / Zocher, G. / Unsoeld, I. / Stec, E. / Li, S.-M. / Heide, L. / Stehle, T.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan dimethylallyltransferase
B: Tryptophan dimethylallyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,07414
Polymers105,9842
Non-polymers1,08912
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint26 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 98.790, 125.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tryptophan dimethylallyltransferase / / L-tryptophan dimethylallyl transferase / DMATS / All-trans-hexaprenyl-diphosphate synthase


Mass: 52992.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q50EL0, 4-dimethylallyltryptophan synthase
#2: Chemical
ChemComp-BU2 / 1,3-BUTANEDIOL / 1,3-Butanediol


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. RESIDUE SER443ALA IS A NATURAL VARIENT IN STRAIN: B5233 / ATCC 13073 OF DMAW_ASPFU ...1. RESIDUE SER443ALA IS A NATURAL VARIENT IN STRAIN: B5233 / ATCC 13073 OF DMAW_ASPFU (UNIPROTKB/SWISS-PROT Q50EL0). 2. AUTHOR CANNOT CLARIFY RESIDUES A 446(PRO) TO 458(LEU) BELONG TO EITHER CHAIN A OR CHAIN B. RESIDUES A 446(PRO) TO 458(LEU) WERE ASSIGNED TO CHAIN A TEMPORARY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% 1,3-butanediol, 50mM sodium L-lactate, 100mM sodium MOPSO pH 7.0, 2mM DTT, vapour diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9395
ROTATING ANODERIGAKU MICROMAX-007 HF21.541789
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 15, 2008
MAR scanner 345 mm plate2IMAGE PLATEDec 23, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111) or Si(311)SINGLE WAVELENGTHMx-ray1
2Cu K alphaSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.93951
21.5417891
ReflectionNumber: 536343 / Rmerge(I) obs: 0.134 / D res high: 2.7 Å / Num. obs: 52137 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
12.0824.7141770.410.038
8.5412.08107310010.039
6.978.54138310010.055
6.046.97165310010.075
5.46.04185110010.085
4.935.4205010010.073
4.574.93226310010.072
4.274.57239610010.074
4.034.27256810010.086
3.824.03271310010.101
3.643.82282510010.115
3.493.64299110010.132
3.353.49313010010.165
3.233.35321710010.197
3.123.23336610010.241
3.023.12344910010.314
2.933.02359810010.355
2.852.93368110010.394
2.772.85376710010.466
2.72.77374697.210.573
ReflectionResolution: 1.76→24.71 Å / Num. obs: 98932 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.14
Reflection shellResolution: 1.76→1.81 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 91.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SHARPphasing
DMphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→24.71 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.333 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2471 2.5 %RANDOM
Rwork0.151 ---
all0.151 98911 --
obs0.152 98911 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 26.02 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 0 72 682 7704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227557
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96610348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95122.825354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.614151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8461562
X-RAY DIFFRACTIONr_chiral_restr0.1030.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215816
X-RAY DIFFRACTIONr_mcbond_it2.26264487
X-RAY DIFFRACTIONr_mcangle_it3.27777342
X-RAY DIFFRACTIONr_scbond_it3.62273070
X-RAY DIFFRACTIONr_scangle_it4.88172956
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 175 -
Rwork0.226 6809 -
all-6984 -
obs--100 %
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)
10.52150.02160.0560.6343-0.2250.8027-0.02940.0189-0.04280.0191-0.0033-0.0042-0.00160.00710.03270.00730.0050.00510.2187-0.0040.261531.60480.95611.329
20.5403-0.2579-0.08181.11390.33830.98910.00140.0088-0.1010.0589-0.05840.09950.1551-0.13510.05710.0455-0.02180.0360.205-0.0080.278113.16473.4547.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 425
2X-RAY DIFFRACTION2B3 - 423

+
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