[English] 日本語
Yorodumi
- PDB-1n22: (+)-Bornyl Diphosphate Synthase: Complex with Mg, pyrophosphate, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n22
Title(+)-Bornyl Diphosphate Synthase: Complex with Mg, pyrophosphate, and (4R)-7-aza-7,8-dihydrolimonene
Components(+)-bornyl diphosphate synthase
KeywordsISOMERASE / terpene synthase fold
Function / homology
Function and homology information


(+)-camphene synthase / (+)-alpha-pinene synthase / (+)-bornyl diphosphate synthase / (+)-camphor biosynthetic process / geranyl-diphosphate cyclase activity / camphene synthase activity / pinene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Terpene synthase, N-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 / Farnesyl Diphosphate Synthase ...Terpene synthase, N-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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(1R)-DIMETHYL-(4-METHYL-CYCLOHEX-3-ENYL)-AMINE / PYROPHOSPHATE 2- / (+)-bornyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSalvia officinalis (garden sage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsWhittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Bornyl diphosphate synthase: Structure and strategy for carbocation manipulation by a terpenoid cyclase
Authors: Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W.
History
DepositionOct 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_conn.ptnr2_label_seq_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: (+)-bornyl diphosphate synthase
B: (+)-bornyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,87213
Polymers128,0712
Non-polymers80111
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-76 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.67, 117.99, 120.29
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer formed by the A and B chains.

-
Components

#1: Protein (+)-bornyl diphosphate synthase


Mass: 64035.664 Da / Num. of mol.: 2 / Fragment: residue 50-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia officinalis (garden sage) / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: UniProt: O81192, (+)-bornyl diphosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-7A8 / (1R)-DIMETHYL-(4-METHYL-CYCLOHEX-3-ENYL)-AMINE / (4R)-7aza-7 / 8-dihydrolimonene / (4R)-7AZA-7,8-DIHYDROLIMONENE


Mass: 139.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17N
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.86 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 8000, glycerol, bis-tris, magnesium chloride, dithiothreitol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlenzyme1drop
21 mMdithiothreitol1drop
320 mMBis-Tris1droppH6.8
410 %(w/v)PEG80001reservoir
515 %(v/v)glycerol1reservoir
62 mMdithiothreitol1reservoiror 1mM potassium mercury thiocyanate
7220 mM1reservoirMgCl2
80.1 MBis-Tris1reservoirpH6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 57537 / % possible obs: 99.1 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 5244 / Rsym value: 0.344 / % possible all: 91.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1N1B

1n1b


Resolution: 2.4→29.14 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2862 5.1 %RANDOM
Rwork0.223 ---
obs0.223 56580 99.9 %-
all-56652 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0805 Å2 / ksol: 0.321517 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---3.87 Å20 Å2
3---0.59 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8719 0 45 170 8934
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 483 5.2 %
Rwork0.284 8792 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4POP.PARAMPOP.TOP
X-RAY DIFFRACTION5TER.PARAMTER.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

+
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