[English] 日本語
Yorodumi
- PDB-3wjn: Crystal structure of Octaprenyl Pyrophosphate synthase from Esche... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wjn
TitleCrystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli with farnesyl S-thiol-pyrophosphate (FSPP)
ComponentsOctaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / site-directed mutagenesis / product chain length
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / Chem-FPS / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHan, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. ...Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. / Guo, R.T. / Ma, Y.H.
CitationJournal: Proteins / Year: 2015
Title: Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms.
Authors: Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Wang, K. / Oldfield, E. / Wang, A.H. / Liang, P.H. / Guo, R.T. / Ma, Y.
History
DepositionOct 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Octaprenyl diphosphate synthase
B: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers73,9392
Non-polymers3981
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-35 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.742, 128.239, 46.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Octaprenyl diphosphate synthase / Octaprenyl Pyrophosphate synthase


Mass: 36969.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O104:H4 str. 2009EL-2071 / Gene: O3O_22640 / Plasmid: pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K0BUH0, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 24% w/v polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 22242 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.454 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJK

3wjk


Resolution: 2.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1051 4.7 %RANDOM
Rwork0.2184 20466 --
obs-21517 96.8 %-
Solvent computationBsol: 22.1852 Å2
Displacement parametersBiso mean: 55.0101 Å2
Baniso -1Baniso -2Baniso -3
1-18.361 Å20 Å20 Å2
2---11.867 Å20 Å2
3----6.494 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 24 153 4823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3291.5
X-RAY DIFFRACTIONc_scbond_it2.0522
X-RAY DIFFRACTIONc_mcangle_it2.2612
X-RAY DIFFRACTIONc_scangle_it3.1652.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree: 0.35 / Rfactor Rwork: 0.302
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2fspp-RT.param
X-RAY DIFFRACTION3water_rep.param

+
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