[English] 日本語
Yorodumi
- PDB-6zzt: Structure of the borneol dehydrogenases of Salvia rosmarinus (hig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zzt
TitleStructure of the borneol dehydrogenases of Salvia rosmarinus (high salt condition)
ComponentsBORNEOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / TERPENOID / ALCOHOL / Borneol / Rossmann-like fold
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesSalvia rosmarinus (rosemary)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDimos, N. / Helmer, C.P.O. / Loll, B.
CitationJournal: Chemcatchem / Year: 2021
Title: A Structural View on the Stereospecificity of Plant Borneol-Type Dehydrogenases.
Authors: Chanique, A.M. / Dimos, N. / Drienovska, I. / Calderini, E. / Pantin, M.P. / Helmer, C.P.O. / Hofer, M. / Sieber, V. / Parra, L.P. / Loll, B. / Kourist, R.
History
DepositionAug 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BORNEOL DEHYDROGENASE
B: BORNEOL DEHYDROGENASE
C: BORNEOL DEHYDROGENASE
D: BORNEOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8727
Polymers121,1384
Non-polymers7343
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-158 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.386, 107.386, 218.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASPASP(chain 'A' and (resid 9 through 54 or resid 56...AA9 - 5430 - 75
12LEULEULEULEU(chain 'A' and (resid 9 through 54 or resid 56...AA5677
13ASNASNASPASP(chain 'A' and (resid 9 through 54 or resid 56...AA59 - 10980 - 130
14LEULEULYSLYS(chain 'A' and (resid 9 through 54 or resid 56...AA111 - 137132 - 158
15GLYGLYPHEPHE(chain 'A' and (resid 9 through 54 or resid 56...AA139 - 190160 - 211
16METMETMETMET(chain 'A' and (resid 9 through 54 or resid 56...AA206227
17GLUGLUSERSER(chain 'A' and (resid 9 through 54 or resid 56...AA208 - 212229 - 233
18VALVALLYSLYS(chain 'A' and (resid 9 through 54 or resid 56...AA214 - 218235 - 239
19ILEILESERSER(chain 'A' and (resid 9 through 54 or resid 56...AA221 - 236242 - 257
110GLUGLUTHRTHR(chain 'A' and (resid 9 through 54 or resid 56...AA238 - 265259 - 286
211ARGARGASPASP(chain 'B' and (resid 9 through 54 or resid 56...BB9 - 5430 - 75
212LEULEULEULEU(chain 'B' and (resid 9 through 54 or resid 56...BB5677
213ASNASNASPASP(chain 'B' and (resid 9 through 54 or resid 56...BB59 - 10980 - 130
214LEULEULYSLYS(chain 'B' and (resid 9 through 54 or resid 56...BB111 - 137132 - 158
215GLYGLYPHEPHE(chain 'B' and (resid 9 through 54 or resid 56...BB139 - 190160 - 211
216METMETMETMET(chain 'B' and (resid 9 through 54 or resid 56...BB206227
217GLUGLUSERSER(chain 'B' and (resid 9 through 54 or resid 56...BB208 - 212229 - 233
218VALVALLYSLYS(chain 'B' and (resid 9 through 54 or resid 56...BB214 - 218235 - 239
219ILEILESERSER(chain 'B' and (resid 9 through 54 or resid 56...BB221 - 236242 - 257
220GLUGLUTHRTHR(chain 'B' and (resid 9 through 54 or resid 56...BB238 - 265259 - 286
321ARGARGASPASP(chain 'C' and (resid 9 through 54 or resid 56...CC9 - 5430 - 75
322LEULEULEULEU(chain 'C' and (resid 9 through 54 or resid 56...CC5677
323ASNASNASPASP(chain 'C' and (resid 9 through 54 or resid 56...CC59 - 10980 - 130
324LEULEULYSLYS(chain 'C' and (resid 9 through 54 or resid 56...CC111 - 137132 - 158
325GLYGLYPHEPHE(chain 'C' and (resid 9 through 54 or resid 56...CC139 - 190160 - 211
326METMETMETMET(chain 'C' and (resid 9 through 54 or resid 56...CC206227
327GLUGLUSERSER(chain 'C' and (resid 9 through 54 or resid 56...CC208 - 212229 - 233
328VALVALLYSLYS(chain 'C' and (resid 9 through 54 or resid 56...CC214 - 218235 - 239
329ILEILESERSER(chain 'C' and (resid 9 through 54 or resid 56...CC221 - 236242 - 257
330GLUGLUTHRTHR(chain 'C' and (resid 9 through 54 or resid 56...CC238 - 265259 - 286
431ARGARGASPASP(chain 'D' and (resid 9 through 54 or resid 56...DD9 - 5430 - 75
432LEULEULEULEU(chain 'D' and (resid 9 through 54 or resid 56...DD5677
433ASNASNASPASP(chain 'D' and (resid 9 through 54 or resid 56...DD59 - 10980 - 130
434LEULEULYSLYS(chain 'D' and (resid 9 through 54 or resid 56...DD111 - 137132 - 158
435GLYGLYPHEPHE(chain 'D' and (resid 9 through 54 or resid 56...DD139 - 190160 - 211
436METMETMETMET(chain 'D' and (resid 9 through 54 or resid 56...DD206227
437GLUGLUSERSER(chain 'D' and (resid 9 through 54 or resid 56...DD208 - 212229 - 233
438VALVALLYSLYS(chain 'D' and (resid 9 through 54 or resid 56...DD214 - 218235 - 239
439ILEILESERSER(chain 'D' and (resid 9 through 54 or resid 56...DD221 - 236242 - 257
440GLUGLUTHRTHR(chain 'D' and (resid 9 through 54 or resid 56...DD238 - 265259 - 286

-
Components

#1: Protein
BORNEOL DEHYDROGENASE


Mass: 30284.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia rosmarinus (rosemary) / Plasmid: pET15a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris/HCl pH 5.5 to pH 7.2, and 2.7 M to 3.2 M NaCl
PH range: 5.5 - 7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9841 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 40188 / % possible obs: 99.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 67.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.152 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 12 % / Rmerge(I) obs: 2.284 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 6358 / CC1/2: 0.612 / Rrim(I) all: 2.386 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bgm

2bgm


Resolution: 2.6→18.14 Å / SU ML: 0.4127 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.3852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 2000 5 %
Rwork0.21 38006 -
obs0.2123 40006 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 46 28 7428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637506
X-RAY DIFFRACTIONf_angle_d0.870310166
X-RAY DIFFRACTIONf_chiral_restr0.05551231
X-RAY DIFFRACTIONf_plane_restr0.00531296
X-RAY DIFFRACTIONf_dihedral_angle_d17.58272638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.47031390.42992646X-RAY DIFFRACTION99.22
2.66-2.730.40321390.40062656X-RAY DIFFRACTION99.79
2.74-2.820.37911400.34822672X-RAY DIFFRACTION99.79
2.82-2.910.37651410.31982683X-RAY DIFFRACTION99.96
2.91-3.010.42491410.2992668X-RAY DIFFRACTION99.96
3.01-3.130.31181410.28542682X-RAY DIFFRACTION99.93
3.13-3.270.38261410.26052680X-RAY DIFFRACTION99.89
3.27-3.440.29781430.25652704X-RAY DIFFRACTION99.93
3.44-3.660.24651420.20662699X-RAY DIFFRACTION99.79
3.66-3.940.23041430.19532718X-RAY DIFFRACTION99.83
3.94-4.330.2551450.17332739X-RAY DIFFRACTION99.9
4.33-4.940.21361440.16232739X-RAY DIFFRACTION99.79
4.94-6.180.2461470.18912789X-RAY DIFFRACTION99.86
6.19-18.140.16961540.16022931X-RAY DIFFRACTION99.84

+
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