[English] 日本語
Yorodumi
- PDB-6vjc: LmFPPS mutant T164Y in complex with 476A, IPP & Ca -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vjc
TitleLmFPPS mutant T164Y in complex with 476A, IPP & Ca
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / FPPS / farnesyl diphosphate synthase / Isoprenoid
Function / homology
Function and homology information


dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase 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
3-butyl-1-(2,2-diphosphonoethyl)pyridinium / ACETATE ION / ISOPENTYL PYROPHOSPHATE / DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsMaheshwari, S. / Kim, Y.S. / Aripirala, S. / Gabelli, S.B.
CitationJournal: Biochemistry / Year: 2020
Title: Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase.
Authors: Maheshwari, S. / Kim, Y.S. / Aripirala, S. / Murphy, M. / Amzel, L.M. / Gabelli, S.B.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,82415
Polymers82,2152
Non-polymers1,60913
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-94 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.525, 85.889, 107.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase


Mass: 41107.273 Da / Num. of mol.: 2 / Mutation: T164Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FPPS, LMJF_22_1360 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QBL1, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase

-
Non-polymers , 6 types, 711 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-476 / 3-butyl-1-(2,2-diphosphonoethyl)pyridinium


Mass: 324.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 100 mM MES, 15-25 % PEG 8000, 100-200 mM CaAcetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 67996 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Χ2: 1.618 / Net I/σ(I): 10.5 / Num. measured all: 422649
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.862.60.68854901.627179.4
1.86-1.943.20.39565441.123195.5
1.94-2.035.20.25869040.8931100
2.03-2.137.10.19768921.0461100
2.13-2.277.10.15669351.2071100
2.27-2.447.20.12569351.4261100
2.44-2.697.20.10469651.5691100
2.69-3.087.30.08369701.8821100
3.08-3.887.20.06570532.3121100
3.88-5070.05673082.488199.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JZX

4jzx


Resolution: 1.8→42.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1812 / WRfactor Rwork: 0.1423 / FOM work R set: 0.8327 / SU B: 2.598 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1219 / SU Rfree: 0.1179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3433 5.1 %RANDOM
Rwork0.1583 ---
obs0.1603 64413 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.1 Å2 / Biso mean: 23.617 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2---0.71 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.8→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 89 698 6549
Biso mean--23.24 33.61 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175592
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.658174
X-RAY DIFFRACTIONr_angle_other_deg1.5851.58112952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58723.113302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.011151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4641526
X-RAY DIFFRACTIONr_chiral_restr0.1330.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026702
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021256
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 199 -
Rwork0.499 3716 -
all-3915 -
obs--76.86 %

+
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