[English] 日本語
Yorodumi
- PDB-5qpo: PanDDA analysis group deposition -- Crystal Structure of T. cruzi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qpo
TitlePanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000574a
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / membrane / metal ion binding
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 1-[(4-fluorophenyl)methyl]benzimidazole / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.6 Å
AuthorsPetrick, J.K. / Nelson, E.R. / Muenzker, L. / Krojer, T. / Douangamath, A. / Brandao-Neto, J. / von Delft, F. / Dekker, C. / Jahnke, W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition - FPPS screened against the DSI Fragment Library
Authors: Petrick, J.K. / Muenzker, L. / von Delft, F. / Jahnke, W.
History
DepositionMar 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8375
Polymers41,3601
Non-polymers4774
Water5,891327
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,67410
Polymers82,7192
Non-polymers9558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7400 Å2
ΔGint-108 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.894, 57.894, 395.786
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Farnesyl diphosphate synthase


Mass: 41359.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WS26
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GQP / 1-[(4-fluorophenyl)methyl]benzimidazole


Mass: 226.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11FN2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.31 Å3/Da / Density % sol: 46.86 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.6→198.04 Å / Num. obs: 54030 / % possible obs: 100 % / Redundancy: 17.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.051 / Rrim(I) all: 0.218 / Net I/σ(I): 7.6 / Num. measured all: 941087 / Scaling rejects: 2010
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.6-1.6414.52.6425614138800.5380.7152.7391
7.16-198.0413.90.0711130381410.0180.07316

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YHK

1yhk


Resolution: 1.6→65.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.759 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 2688 5.2 %RANDOM
Rwork0.2265 ---
obs0.2287 49443 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.02 Å2 / Biso mean: 18.808 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.6→65.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 31 328 3230
Biso mean--36.5 27.95 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023320
X-RAY DIFFRACTIONr_bond_other_d0.0020.022899
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9684296
X-RAY DIFFRACTIONr_angle_other_deg1.13436732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.444144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9415548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8981515
X-RAY DIFFRACTIONr_chiral_restr0.1350.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023763
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02676
X-RAY DIFFRACTIONr_mcbond_it1.6931.7011610
X-RAY DIFFRACTIONr_mcbond_other1.6931.7021611
X-RAY DIFFRACTIONr_mcangle_it2.5142.5131932
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 205 -
Rwork0.349 3383 -
all-3588 -
obs--92.62 %

+
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