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- PDB-6zyz: Structure of the borneol dehydrogenases of Salvia rosmarinus with NAD+ -

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Basic information

Entry
Database: PDB / ID: 6zyz
TitleStructure of the borneol dehydrogenases of Salvia rosmarinus with NAD+
ComponentsBorneol dehydrogenase from salvia rosmarinus
KeywordsOXIDOREDUCTASE / TERPENOID / ALCOHOL / Borneol / Rossmann-like fold
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PXN
Function and homology information
Biological speciesSalvia rosmarinus (rosemary)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 3, 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 from salvia rosmarinus
B: Borneol dehydrogenase from salvia rosmarinus
C: Borneol dehydrogenase from salvia rosmarinus
D: Borneol dehydrogenase from salvia rosmarinus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,56411
Polymers121,1384
Non-polymers3,4267
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-166 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.841, 196.841, 65.267
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,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 46 or resid 48...AA9 - 4630 - 67
12LEULEUASPASP(chain 'A' and (resid 9 through 46 or resid 48...AA48 - 5469 - 75
13LEULEULEULEU(chain 'A' and (resid 9 through 46 or resid 48...AA5677
14ASNASNILEILE(chain 'A' and (resid 9 through 46 or resid 48...AA59 - 6080 - 81
15TYRTYRVALVAL(chain 'A' and (resid 9 through 46 or resid 48...AA62 - 7383 - 94
16ALAALAASPASP(chain 'A' and (resid 9 through 46 or resid 48...AA75 - 10996 - 130
17LEULEUGLUGLU(chain 'A' and (resid 9 through 46 or resid 48...AA111 - 150132 - 171
18ALAALALYSLYS(chain 'A' and (resid 9 through 46 or resid 48...AA152 - 171173 - 192
19LEULEUTHRTHR(chain 'A' and (resid 9 through 46 or resid 48...AA173 - 194194 - 215
110METMETPHEPHE(chain 'A' and (resid 9 through 46 or resid 48...AA206 - 207227 - 228
111GLYGLYSERSER(chain 'A' and (resid 9 through 46 or resid 48...AA209 - 212230 - 233
112VALVALTHRTHR(chain 'A' and (resid 9 through 46 or resid 48...AA214 - 265235 - 286
213ARGARGASPASP(chain 'B' and (resid 9 through 46 or resid 48...BB9 - 4630 - 67
214LEULEUASPASP(chain 'B' and (resid 9 through 46 or resid 48...BB48 - 5469 - 75
215LEULEULEULEU(chain 'B' and (resid 9 through 46 or resid 48...BB5677
216ASNASNILEILE(chain 'B' and (resid 9 through 46 or resid 48...BB59 - 6080 - 81
217TYRTYRVALVAL(chain 'B' and (resid 9 through 46 or resid 48...BB62 - 7383 - 94
218ALAALAASPASP(chain 'B' and (resid 9 through 46 or resid 48...BB75 - 10996 - 130
219LEULEUGLUGLU(chain 'B' and (resid 9 through 46 or resid 48...BB111 - 150132 - 171
220ALAALALYSLYS(chain 'B' and (resid 9 through 46 or resid 48...BB152 - 171173 - 192
221LEULEUTHRTHR(chain 'B' and (resid 9 through 46 or resid 48...BB173 - 194194 - 215
222METMETPHEPHE(chain 'B' and (resid 9 through 46 or resid 48...BB206 - 207227 - 228
223GLYGLYSERSER(chain 'B' and (resid 9 through 46 or resid 48...BB209 - 212230 - 233
224VALVALTHRTHR(chain 'B' and (resid 9 through 46 or resid 48...BB214 - 265235 - 286
325ARGARGASPASP(chain 'C' and (resid 9 through 46 or resid 48...CC9 - 4630 - 67
326LEULEUASPASP(chain 'C' and (resid 9 through 46 or resid 48...CC48 - 5469 - 75
327LEULEULEULEU(chain 'C' and (resid 9 through 46 or resid 48...CC5677
328ASNASNILEILE(chain 'C' and (resid 9 through 46 or resid 48...CC59 - 6080 - 81
329TYRTYRVALVAL(chain 'C' and (resid 9 through 46 or resid 48...CC62 - 7383 - 94
330ALAALAASPASP(chain 'C' and (resid 9 through 46 or resid 48...CC75 - 10996 - 130
331LEULEUGLUGLU(chain 'C' and (resid 9 through 46 or resid 48...CC111 - 150132 - 171
332ALAALALYSLYS(chain 'C' and (resid 9 through 46 or resid 48...CC152 - 171173 - 192
333LEULEUTHRTHR(chain 'C' and (resid 9 through 46 or resid 48...CC173 - 194194 - 215
334METMETPHEPHE(chain 'C' and (resid 9 through 46 or resid 48...CC206 - 207227 - 228
335GLYGLYSERSER(chain 'C' and (resid 9 through 46 or resid 48...CC209 - 212230 - 233
336VALVALTHRTHR(chain 'C' and (resid 9 through 46 or resid 48...CC214 - 265235 - 286
437ARGARGASPASP(chain 'D' and (resid 9 through 46 or resid 48...DD9 - 4630 - 67
438LEULEUASPASP(chain 'D' and (resid 9 through 46 or resid 48...DD48 - 5469 - 75
439LEULEULEULEU(chain 'D' and (resid 9 through 46 or resid 48...DD5677
440ASNASNILEILE(chain 'D' and (resid 9 through 46 or resid 48...DD59 - 6080 - 81
441TYRTYRVALVAL(chain 'D' and (resid 9 through 46 or resid 48...DD62 - 7383 - 94
442ALAALAASPASP(chain 'D' and (resid 9 through 46 or resid 48...DD75 - 10996 - 130
443LEULEUGLUGLU(chain 'D' and (resid 9 through 46 or resid 48...DD111 - 150132 - 171
444ALAALALYSLYS(chain 'D' and (resid 9 through 46 or resid 48...DD152 - 171173 - 192
445LEULEUTHRTHR(chain 'D' and (resid 9 through 46 or resid 48...DD173 - 194194 - 215
446METMETPHEPHE(chain 'D' and (resid 9 through 46 or resid 48...DD206 - 207227 - 228
447GLYGLYSERSER(chain 'D' and (resid 9 through 46 or resid 48...DD209 - 212230 - 233
448VALVALTHRTHR(chain 'D' and (resid 9 through 46 or resid 48...DD214 - 265235 - 286

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Components

#1: Protein
Borneol dehydrogenase from salvia rosmarinus


Mass: 30284.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia rosmarinus (rosemary) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O8
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2
Details: The NAD+ cofactor is differently occupied which is reflected in the quality of the electron density
Comment: NAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% 5/4 PO/OH 0.2M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 66509 / % possible obs: 99.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 40.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.218 / Net I/σ(I): 9.88
Reflection shellResolution: 2.27→2.41 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.853 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 10563 / CC1/2: 0.509 / Rrim(I) all: 1.975 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bgm

2bgm


Resolution: 2.27→47.28 Å / SU ML: 0.2899 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 2100 3.16 %
Rwork0.1965 64384 -
obs0.1977 66484 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.82 Å2
Refinement stepCycle: LAST / Resolution: 2.27→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7571 0 227 196 7994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717967
X-RAY DIFFRACTIONf_angle_d0.948610825
X-RAY DIFFRACTIONf_chiral_restr0.05521305
X-RAY DIFFRACTIONf_plane_restr0.00531363
X-RAY DIFFRACTIONf_dihedral_angle_d11.9934629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.34941340.31034118X-RAY DIFFRACTION96.16
2.33-2.390.34811400.29834283X-RAY DIFFRACTION99.91
2.39-2.450.33171380.28124219X-RAY DIFFRACTION99.89
2.45-2.520.3061400.2534310X-RAY DIFFRACTION99.93
2.52-2.60.31421390.2524264X-RAY DIFFRACTION99.98
2.6-2.70.27561400.24974287X-RAY DIFFRACTION100
2.7-2.80.30491400.23034288X-RAY DIFFRACTION99.91
2.8-2.930.25771390.21754269X-RAY DIFFRACTION100
2.93-3.090.31841400.2034308X-RAY DIFFRACTION99.98
3.09-3.280.2511410.20724305X-RAY DIFFRACTION99.98
3.28-3.530.21961390.19244278X-RAY DIFFRACTION100
3.53-3.890.191410.16874322X-RAY DIFFRACTION99.96
3.89-4.450.19981410.16294323X-RAY DIFFRACTION100
4.45-5.610.1951420.16234360X-RAY DIFFRACTION99.93
5.61-47.280.18911460.17414450X-RAY DIFFRACTION99.83

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