[English] 日本語
Yorodumi
- PDB-6wkd: Crystal structure of pentalenene synthase complexed with 12,13-di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wkd
TitleCrystal structure of pentalenene synthase complexed with 12,13-difluorofarnesyl diphosphate
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / LYASE/INHIBITOR / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding / LYASE-INHIBITOR complex
Function / homology
Function and homology information


pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-FDF / Pentalenene synthase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPrem Kumar, R. / Matos, J.O. / Oprian, D.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007596 United States
CitationJournal: Biochemistry / Year: 2020
Title: Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase.
Authors: Matos, J.O. / Kumar, R.P. / Ma, A.C. / Patterson, M. / Krauss, I.J. / Oprian, D.D.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7527
Polymers76,1012
Non-polymers6515
Water6,539363
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6095
Polymers38,0501
Non-polymers5594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1432
Polymers38,0501
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.467, 182.467, 56.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Pentalenene synthase / PS / Pentalenolactone biosynthesis protein A / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 38050.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: penA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q55012, pentalenene synthase
#2: Chemical ChemComp-FDF / (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 418.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26F2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.8-1.2 M sodium tartrate, 100 mM Tris, and 5 mM DTT
PH range: 7.5 - 9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2018 / Details: Mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 54634 / % possible obs: 99.9 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 21 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7917 / CC1/2: 0.75 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 2.2→19.971 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 2780 5.09 %
Rwork0.2005 51836 -
obs0.2015 54616 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.1 Å2 / Biso mean: 48.2834 Å2 / Biso min: 25.01 Å2
Refinement stepCycle: final / Resolution: 2.2→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 40 363 5014
Biso mean--61.88 52.31 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034755
X-RAY DIFFRACTIONf_angle_d0.536450
X-RAY DIFFRACTIONf_dihedral_angle_d18.312842
X-RAY DIFFRACTIONf_chiral_restr0.037682
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.23790.33911380.29342582
2.2379-2.27850.3231150.31762594
2.2785-2.32230.30621180.27512581
2.3223-2.36960.30941460.26022565
2.3696-2.42110.2731530.24032525
2.4211-2.47730.24321470.24382579
2.4773-2.53910.27121370.23562606
2.5391-2.60760.31311260.22542570
2.6076-2.68420.25651340.23472608
2.6842-2.77060.2983990.2392591
2.7706-2.86940.30611350.22892574
2.8694-2.98390.25031610.22632590
2.9839-3.11920.24871510.22782572
3.1192-3.2830.25981570.21182566
3.283-3.48770.21461490.20412582
3.4877-3.75530.21510.1762600
3.7553-4.13020.18291280.16632607
4.1302-4.72090.17681300.15542625
4.7209-5.92210.17611500.18032619
5.9221-19.9710.17791550.18852700

+
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