[English] 日本語
Yorodumi
- PDB-9c7m: Crystal structure of pentalenene synthase variant F76A complexed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c7m
TitleCrystal structure of pentalenene synthase variant F76A complexed with 12,13-difluorofarnesyl diphosphate
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / Terpene synthase / Cyclase / Sesquiterpene synthase / complex / Inhibitor / Fluoro analog
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 exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPrem Kumar, R. / Ellenburg, W.H. / Oprian, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2024
Title: Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction.
Authors: Kumar, R.P. / Matos, J.O. / Black, B.Y. / Ellenburg, W.H. / Chen, J. / Patterson, M. / Gehtman, J.A. / Theobald, D.L. / Krauss, I.J. / Oprian, D.D.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
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)76,4406
Polymers75,9492
Non-polymers4914
Water97354
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4665
Polymers37,9741
Non-polymers4914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)37,9741
Polymers37,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.530, 180.530, 55.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

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


Mass: 37974.316 Da / Num. of mol.: 2 / Mutation: F76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: penA / Production host: Escherichia coli (E. coli) / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, containing 2 M ammonium sulfate and 2% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 30519 / % possible obs: 99.7 % / Redundancy: 20.9 % / Biso Wilson estimate: 72.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 18.9
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 21.8 % / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4036 / CC1/2: 0.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.8 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1535 5.04 %
Rwork0.1982 --
obs0.1997 30478 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 29 54 5010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025073
X-RAY DIFFRACTIONf_angle_d0.4836890
X-RAY DIFFRACTIONf_dihedral_angle_d13.3051855
X-RAY DIFFRACTIONf_chiral_restr0.036722
X-RAY DIFFRACTIONf_plane_restr0.005919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.33441390.30212586X-RAY DIFFRACTION100
2.74-2.830.32471430.28252607X-RAY DIFFRACTION100
2.83-2.950.31061630.2622593X-RAY DIFFRACTION100
2.95-3.080.28431350.25892596X-RAY DIFFRACTION100
3.08-3.240.27121180.24392627X-RAY DIFFRACTION100
3.24-3.440.26831590.23152604X-RAY DIFFRACTION100
3.44-3.710.26451280.20352647X-RAY DIFFRACTION100
3.71-4.080.21761390.19232625X-RAY DIFFRACTION100
4.08-4.660.2091450.17242644X-RAY DIFFRACTION100
4.66-5.850.21121100.19312694X-RAY DIFFRACTION100
5.85-19.80.18561560.16422720X-RAY DIFFRACTION100

+
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