[English] 日本語
Yorodumi
- PDB-9d28: Crystal structure of (+)-sabinene synthase from Thuja plicata -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d28
TitleCrystal structure of (+)-sabinene synthase from Thuja plicata
ComponentsSabinene synthase
KeywordsLYASE / Biosynthesis / Terpene / Cyclization
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / : / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Biological speciesThuja plicata (giant arborvitae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGaynes, M.N. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2024
Title: Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product.
Authors: Gaynes, M.N. / Osika, K.R. / Christianson, D.W.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Dec 11, 2024Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Sabinene synthase
A: Sabinene synthase
C: Sabinene synthase
D: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)256,4654
Polymers256,4654
Non-polymers00
Water3,513195
1
B: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.290, 89.810, 194.520
Angle α, β, γ (deg.)90.000, 134.890, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
Sabinene synthase


Mass: 64116.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thuja plicata (giant arborvitae) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9WS05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/ml sabinene synthase, 3.5 M sodium formate (pH 7.0), 10 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.32→96.81 Å / Num. obs: 143268 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 50.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Net I/σ(I): 13.4
Reflection shellResolution: 2.32→2.4 Å / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14298 / CC1/2: 0.811 / Rpim(I) all: 0.418

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→96.81 Å / SU ML: 0.3208 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 3875 1.38 %
Rwork0.2127 276878 -
obs0.213 143073 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.89 Å2
Refinement stepCycle: LAST / Resolution: 2.32→96.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16050 0 0 195 16245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007216400
X-RAY DIFFRACTIONf_angle_d0.900922317
X-RAY DIFFRACTIONf_chiral_restr0.04982479
X-RAY DIFFRACTIONf_plane_restr0.00692900
X-RAY DIFFRACTIONf_dihedral_angle_d14.35235836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.33681340.3519918X-RAY DIFFRACTION99.48
2.35-2.380.3841420.32729898X-RAY DIFFRACTION99.35
2.38-2.410.37471440.31179937X-RAY DIFFRACTION99.5
2.41-2.440.2921420.30579903X-RAY DIFFRACTION99.26
2.44-2.480.2891360.30039887X-RAY DIFFRACTION99.1
2.48-2.510.3181430.29499938X-RAY DIFFRACTION99.33
2.51-2.550.32731330.29129853X-RAY DIFFRACTION98.61
2.55-2.60.34211440.2819817X-RAY DIFFRACTION98.04
2.6-2.640.30181380.27799812X-RAY DIFFRACTION97.71
2.64-2.690.32621420.26249580X-RAY DIFFRACTION96.72
2.69-2.740.27221360.27399986X-RAY DIFFRACTION99.39
2.74-2.80.33611480.26429907X-RAY DIFFRACTION99.49
2.8-2.860.31521360.25759887X-RAY DIFFRACTION99.41
2.86-2.920.26431370.2589992X-RAY DIFFRACTION99.68
2.92-30.32271480.25979972X-RAY DIFFRACTION99.43
3-3.080.26181420.25619918X-RAY DIFFRACTION99.72
3.08-3.170.25131300.26359908X-RAY DIFFRACTION99.37
3.17-3.270.29071270.23239936X-RAY DIFFRACTION99.23
3.27-3.390.21381460.2329952X-RAY DIFFRACTION99.48
3.39-3.520.23851400.2119831X-RAY DIFFRACTION98.64
3.52-3.680.26991360.20199973X-RAY DIFFRACTION99.16
3.68-3.880.23621300.18699713X-RAY DIFFRACTION97.47
3.88-4.120.23061420.18519916X-RAY DIFFRACTION99.12
4.12-4.440.19071230.16169921X-RAY DIFFRACTION99.62
4.44-4.880.18421410.16919961X-RAY DIFFRACTION99.59
4.88-5.590.22771500.18889948X-RAY DIFFRACTION99.4
5.59-7.040.20261260.21269904X-RAY DIFFRACTION99.36
7.04-96.810.14721390.15489710X-RAY DIFFRACTION96.91

+
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