[English] 日本語
Yorodumi
- PDB-6se2: Trypanosoma cruzi farnesyl diphosphate synthase apo structure wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6se2
TitleTrypanosoma cruzi farnesyl diphosphate synthase apo structure with zinc ions
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / Farnesyl diphosphate synthase (FDPS) / Farnesyl pyrophosphate synthase (FPPS) / Trypanosoma cruzi / apo structure / zinc ions
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / membrane / 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
Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Union
CitationJournal: To Be Published
Title: Trypanosoma cruzi farnesyl diphosphate synthase apo structure with zinc ions
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 29, 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 diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4324
Polymers41,2051
Non-polymers2273
Water5,026279
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8658
Polymers82,4112
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6660 Å2
ΔGint-195 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.935, 57.935, 397.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

21A-768-

HOH

-
Components

#1: Protein Farnesyl diphosphate synthase


Mass: 41205.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WS26
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 4mM ZnSO4+ 8 mM MES pH:6.50, 12.36% PEG MME 550, 11.57% Glycerol. crystal obtained by microseeding: 160mM (NH4)2SO4, 80mM NaOAc pH:5.00, 20% PEG 4000, 20% Glycerol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→397.468 Å / Num. obs: 71946 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 0.999 / Rsym value: 0.053 / Net I/σ(I): 32.83
Reflection shellResolution: 1.45→1.54 Å / Mean I/σ(I) obs: 6.42 / Num. unique obs: 11290 / CC1/2: 0.961 / Rsym value: 0.475 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yhl

1yhl


Resolution: 1.45→49.78 Å / SU ML: 0.1133 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.4729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 3598 5 %
Rwork0.1699 68345 -
obs0.1708 71943 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 1.45→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 7 279 3077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762907
X-RAY DIFFRACTIONf_angle_d0.91333968
X-RAY DIFFRACTIONf_chiral_restr0.0698449
X-RAY DIFFRACTIONf_plane_restr0.0061511
X-RAY DIFFRACTIONf_dihedral_angle_d19.12361022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.2561310.21022477X-RAY DIFFRACTION99.5
1.47-1.490.21261370.18662607X-RAY DIFFRACTION100
1.49-1.510.20391330.1792521X-RAY DIFFRACTION100
1.51-1.530.18441370.17192602X-RAY DIFFRACTION100
1.53-1.560.20951340.17742547X-RAY DIFFRACTION100
1.56-1.580.1641350.17162574X-RAY DIFFRACTION100
1.58-1.610.20691370.1762604X-RAY DIFFRACTION100
1.61-1.640.21751350.16992557X-RAY DIFFRACTION100
1.64-1.670.23331360.16682583X-RAY DIFFRACTION100
1.67-1.710.17911370.17182608X-RAY DIFFRACTION100
1.71-1.740.1921350.1682558X-RAY DIFFRACTION100
1.74-1.780.18361360.16662591X-RAY DIFFRACTION99.96
1.78-1.830.17851370.16282595X-RAY DIFFRACTION100
1.83-1.880.18281360.16742592X-RAY DIFFRACTION100
1.88-1.930.20461390.16592643X-RAY DIFFRACTION100
1.93-1.990.16471360.1692592X-RAY DIFFRACTION100
1.99-2.070.2121380.16422620X-RAY DIFFRACTION100
2.07-2.150.19391390.15632625X-RAY DIFFRACTION100
2.15-2.250.18131380.15592629X-RAY DIFFRACTION100
2.25-2.360.15631380.14362624X-RAY DIFFRACTION100
2.36-2.510.14511420.15162699X-RAY DIFFRACTION100
2.51-2.710.16971390.15962641X-RAY DIFFRACTION100
2.71-2.980.18641420.17332696X-RAY DIFFRACTION100
2.98-3.410.20211450.17612748X-RAY DIFFRACTION100
3.41-4.30.18751460.16352772X-RAY DIFFRACTION100
4.3-49.780.19191600.19473040X-RAY DIFFRACTION99.94
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)
11.50766600516-0.1562272597630.3452243065560.4836817079370.0909360464160.626550222394-0.05821985647060.04043368034020.191021694746-0.0151227873468-0.0110185723615-0.0556078515124-0.05665571499250.0623469112354-0.0005935767036150.1033411821050.01415376344620.01363248166910.1183240269840.02465442506210.146578275661-3.70227483831-14.7720887299-33.092269474
20.340142878253-0.04754074462190.10700273560.383079639601-0.02569389827510.417688520119-0.00558622868234-0.171233475783-0.02439842825220.0463562549358-0.009959515497710.03427566707750.0360350504887-0.02285994306666.10142832353E-50.1428229744620.02806759396680.006280594123370.2053630677380.001800957485240.135577498901-11.7145724251-26.3686537294-18.3876171946
31.110477372710.469269996712-0.6791743593940.02420051319570.1166298414560.8464110856750.0209808296637-0.162622225960.408310745975-0.006755995064110.04744254282240.0682136570411-0.2346890807620.01552302600460.0001539935831090.2919296975890.000702176120813-0.009477546531540.349410207358-0.03698178960630.2963321405-13.7012179422-14.4656519158-6.76138419316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 360 )

+
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