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- PDB-6zzt: Structure of the borneol dehydrogenases of Salvia rosmarinus (hig... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Chloride


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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