[English] 日本語
Yorodumi
- PDB-3sdr: Structure of a three-domain sesquiterpene synthase: a prospective... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sdr
TitleStructure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production
ComponentsAlpha-bisabolene synthase
KeywordsLYASE / TERPENE SYNTHASE
Function / homology
Function and homology information


alpha-bisabolene synthase / alpha-bisabolene synthase activity / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Glycosyltransferase - #160 / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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 / Farnesyl Diphosphate Synthase ...Glycosyltransferase - #160 / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PAMIDRONATE / Alpha-bisabolene synthase
Similarity search - Component
Biological speciesAbies grandis (grand fir)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 1.86 Å
AuthorsMcAndrew, R.P. / Peralta-Yahya, P.P. / DeGiovanni, A. / Pereira, J.H. / Hadi, M.Z. / Keasling, J.D. / Adams, P.D.
CitationJournal: Structure / Year: 2011
Title: Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production.
Authors: McAndrew, R.P. / Peralta-Yahya, P.P. / DeGiovanni, A. / Pereira, J.H. / Hadi, M.Z. / Keasling, J.D. / Adams, P.D.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-bisabolene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1996
Polymers93,8551
Non-polymers3435
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.458, 54.479, 126.607
Angle α, β, γ (deg.)90.00, 119.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1108-

HOH

-
Components

#1: Protein Alpha-bisabolene synthase / / (E)-alpha-bisabolene synthase / AgfEabis


Mass: 93855.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abies grandis (grand fir) / Gene: ag1 / Plasmid: PSKB33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O81086, alpha-bisabolene synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID / Pamidronic acid


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 MM TRIS, 100 MM NACL, AND 23% (W/V) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 79523 / Num. obs: 79327 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.072 / Net I/σ(I): 26.3
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.44 / Rsym value: 0.833 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
BOSdata collection
Auto-Rickshawphasing
RESOLVEmodel building
PHASERphasing
PHENIX(phenix.refine: dev_778)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 1.86→38.292 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 1999 2.52 %
Rwork0.1788 --
obs0.1796 79277 99.31 %
all-79523 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.924 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3886 Å2-0 Å20.7786 Å2
2--12.1749 Å20 Å2
3----9.7863 Å2
Refinement stepCycle: LAST / Resolution: 1.86→38.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6311 0 17 506 6834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096508
X-RAY DIFFRACTIONf_angle_d0.9448847
X-RAY DIFFRACTIONf_dihedral_angle_d12.7282437
X-RAY DIFFRACTIONf_chiral_restr0.067968
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.89580.30541310.29225093X-RAY DIFFRACTION93
1.8958-1.9470.35171430.27215500X-RAY DIFFRACTION99
1.947-2.00430.26961430.21345486X-RAY DIFFRACTION100
2.0043-2.0690.22821420.19895517X-RAY DIFFRACTION100
2.069-2.1430.23261420.18925480X-RAY DIFFRACTION100
2.143-2.22870.24651440.18485537X-RAY DIFFRACTION100
2.2287-2.33020.23651420.18825505X-RAY DIFFRACTION100
2.3302-2.4530.22611440.18135564X-RAY DIFFRACTION100
2.453-2.60670.20651430.17625554X-RAY DIFFRACTION100
2.6067-2.80790.23521430.18115530X-RAY DIFFRACTION100
2.8079-3.09030.20121440.19455561X-RAY DIFFRACTION100
3.0903-3.53720.21621440.1825588X-RAY DIFFRACTION100
3.5372-4.45540.16881460.15595612X-RAY DIFFRACTION100
4.4554-38.30070.19991480.16025751X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.6070.34614.40621.2393-0.10374.5928-0.03610.6142-0.264-0.09390.0926-0.1704-0.01620.57160.00830.2859-0.02320.03470.1947-0.04130.239596.546225.253210.6651
22.6143-0.39120.4351.5549-0.05392.19780.00830.2249-0.3168-0.121-0.00940.05740.6197-0.22320.00780.3751-0.1071-0.01480.0924-0.05890.220957.63323.73939.2907
34.4373-3.612-0.74764.0282-0.65511.5854-0.3835-0.6249-0.50880.46450.46180.43080.334-0.0055-0.07130.3319-0.12910.0070.32080.05530.234650.93913.091526.9767
44.53740.2572-1.621.11880.22184.7730.04250.04990.1548-0.0679-0.03760.15450.1374-0.4852-0.0090.2085-0.0476-0.02230.1977-0.00190.221650.546519.841513.9086
54.50680.5174-0.28161.74480.49482.3085-0.0466-0.31350.3240.0067-0.00580.303-0.0306-0.20290.05290.20010.02590.00040.1236-0.04070.229371.360530.132222.9616
62.06750.5160.03827.02032.06592.66170.1667-0.43-0.04910.6272-0.2020.17470.3704-0.07690.06440.2417-0.06290.00630.22650.01610.159773.096716.660733.4529
71.87690.67730.40360.57110.14210.52960.0772-0.2955-0.14710.0442-0.0706-0.10730.05730.1417-0.02530.1710.00130.00990.2376-0.00630.181199.501326.381128.2417
81.7269-0.4646-0.01470.70560.08361.2603-0.0217-0.69770.4190.1808-0.0032-0.07-0.1620.23960.0620.2046-0.0899-0.00450.4851-0.13230.2278106.882545.222441.5049
92.3392-0.1742-0.56220.69620.01375.41740.1672-1.1361-0.63480.2053-0.12890.11570.4807-0.14850.11140.15-0.12360.10160.52660.00840.143290.403432.467250.0875
103.2753-0.975-0.6083.18131.28175.136-0.1313-0.6118-0.46910.69250.0216-0.08510.64640.18350.12960.2134-0.0457-0.0230.35580.04130.311396.749925.152633.3522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 36:73)
2X-RAY DIFFRACTION2(chain A and resid 74:195)
3X-RAY DIFFRACTION3(chain A and resid 196:223)
4X-RAY DIFFRACTION4(chain A and resid 224:293)
5X-RAY DIFFRACTION5(chain A and resid 294:382)
6X-RAY DIFFRACTION6(chain A and resid 383:445)
7X-RAY DIFFRACTION7(chain A and resid 446:580)
8X-RAY DIFFRACTION8(chain A and resid 581:702)
9X-RAY DIFFRACTION9(chain A and resid 703:770)
10X-RAY DIFFRACTION10(chain A and resid 771:817)

+
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