[English] 日本語
Yorodumi
- PDB-6sii: T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sii
TitleT. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chlorobenzyl)piperidin-4-amine
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / sterol biosynthesis / homodimer / farnesyl pyrophosphate synthase / Trypanosoma brucei
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-LEZ / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Other government675899 Switzerland
Marie Sklodowska-Curie Actions, FragNET ITN
CitationJournal: To Be Published
Title: T. brucei FPPS
Authors: Muenzker, L. / Jahnke, W.
History
DepositionAug 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6153
Polymers42,1691
Non-polymers4462
Water00
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2306
Polymers84,3382
Non-polymers8924
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.631, 61.631, 342.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 42169.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GP is an expression tag / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09
#2: Chemical ChemComp-LEZ / ~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine


Mass: 353.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24ClN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.12 M CsCl 12 % w/v PEG 3350, 12 % v/v DMSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.326→57.041 Å / Num. obs: 17624 / % possible obs: 99.4 % / Redundancy: 18.5 % / Biso Wilson estimate: 79.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Rsym value: 0.113 / Net I/σ(I): 15.1 / Num. measured all: 326497
Reflection shellResolution: 2.326→2.366 Å / Redundancy: 19.6 % / Rmerge(I) obs: 12.631 / Mean I/σ(I) obs: 0.3 / Num. measured all: 48808 / Num. unique obs: 2512 / CC1/2: 0.59 / Rpim(I) all: 1.983 / Rrim(I) all: 8.823 / Rsym value: 12.631 / Net I/σ(I) obs: 0.4 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å57.04 Å

-
Processing

Software
NameVersionClassification
BUSTERrefinement
XDS20180126data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4ryp

4ryp


Resolution: 2.33→57.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.276 832 5.01 %RANDOM
Rwork0.25 ---
obs0.252 16603 93.6 %-
Displacement parametersBiso max: 228.35 Å2 / Biso mean: 121.49 Å2 / Biso min: 64.15 Å2
Baniso -1Baniso -2Baniso -3
1--4.1842 Å20 Å20 Å2
2---4.1842 Å20 Å2
3---8.3684 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.33→57.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 31 0 2650
Biso mean--119.51 --
Num. residues----328
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d949SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it2702HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion338SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3115SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2702HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3648HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion18.44
LS refinement shellResolution: 2.33→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 41
RfactorNum. reflection% reflection
Rfree0.6311 17 4.2 %
Rwork0.3485 388 -
all0.3606 405 -
obs--36.88 %
Refinement TLS params.Method: refined / Origin x: 3.4606 Å / Origin y: 11.916 Å / Origin z: -11.451 Å
111213212223313233
T0.3582 Å2-0.0271 Å2-0.0133 Å2--0.1289 Å20.0896 Å2---0.3311 Å2
L1.0762 °20.245 °2-1.2262 °2-2.5632 °21.3147 °2--12.6176 °2
S-0.367 Å °0.1769 Å °0.0524 Å °-0.3433 Å °0.5399 Å °0.1587 Å °-1.2298 Å °-0.0469 Å °-0.1729 Å °
Refinement TLS groupSelection details: { A|* }

+
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