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- PDB-6zz0: Structure of the borneol dehydrogenase of Salvia rosmarinus (apo) -

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Basic information

Entry
Database: PDB / ID: 6zz0
TitleStructure of the borneol dehydrogenase of Salvia rosmarinus (apo)
ComponentsBorneol Dehydrogenase (salvia rosmarinus) apo structure
KeywordsOXIDOREDUCTASE / TERPENOID / ALCOHOL / Borneol / Rossmann-like fold
Biological speciesSalvia rosmarinus (rosemary)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 (salvia rosmarinus) apo structure
B: Borneol Dehydrogenase (salvia rosmarinus) apo structure
C: Borneol Dehydrogenase (salvia rosmarinus) apo structure
D: Borneol Dehydrogenase (salvia rosmarinus) apo structure


Theoretical massNumber of molelcules
Total (without water)121,1384
Polymers121,1384
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-139 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.180, 108.180, 230.366
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
11ARGARGALAALA(chain 'A' and (resid 9 through 54 or resid 56...AA9 - 5330 - 74
12LEULEULEULEU(chain 'A' and (resid 9 through 54 or resid 56...AA5677
13ASNASNGLNGLN(chain 'A' and (resid 9 through 54 or resid 56...AA59 - 7280 - 93
14ALAALALYSLYS(chain 'A' and (resid 9 through 54 or resid 56...AA75 - 10896 - 129
15LEULEUPHEPHE(chain 'A' and (resid 9 through 54 or resid 56...AA111 - 190132 - 211
16GLUGLUMETMET(chain 'A' and (resid 9 through 54 or resid 56...AA208 - 211229 - 232
17VALVALLYSLYS(chain 'A' and (resid 9 through 54 or resid 56...AA214 - 218235 - 239
18ILEILEALAALA(chain 'A' and (resid 9 through 54 or resid 56...AA221 - 235242 - 256
19GLUGLUILEILE(chain 'A' and (resid 9 through 54 or resid 56...AA238 - 264259 - 285
210ARGARGALAALA(chain 'B' and (resid 9 through 54 or resid 56...BB9 - 5330 - 74
211LEULEULEULEU(chain 'B' and (resid 9 through 54 or resid 56...BB5677
212ASNASNGLNGLN(chain 'B' and (resid 9 through 54 or resid 56...BB59 - 7280 - 93
213ALAALALYSLYS(chain 'B' and (resid 9 through 54 or resid 56...BB75 - 10896 - 129
214LEULEUPHEPHE(chain 'B' and (resid 9 through 54 or resid 56...BB111 - 190132 - 211
215GLUGLUMETMET(chain 'B' and (resid 9 through 54 or resid 56...BB208 - 211229 - 232
216VALVALLYSLYS(chain 'B' and (resid 9 through 54 or resid 56...BB214 - 218235 - 239
217ILEILEALAALA(chain 'B' and (resid 9 through 54 or resid 56...BB221 - 235242 - 256
218GLUGLUILEILE(chain 'B' and (resid 9 through 54 or resid 56...BB238 - 264259 - 285
319ARGARGALAALA(chain 'C' and (resid 9 through 54 or resid 56...CC9 - 5330 - 74
320LEULEULEULEU(chain 'C' and (resid 9 through 54 or resid 56...CC5677
321ASNASNGLNGLN(chain 'C' and (resid 9 through 54 or resid 56...CC59 - 7280 - 93
322ALAALALYSLYS(chain 'C' and (resid 9 through 54 or resid 56...CC75 - 10896 - 129
323LEULEUPHEPHE(chain 'C' and (resid 9 through 54 or resid 56...CC111 - 190132 - 211
324GLUGLUMETMET(chain 'C' and (resid 9 through 54 or resid 56...CC208 - 211229 - 232
325VALVALLYSLYS(chain 'C' and (resid 9 through 54 or resid 56...CC214 - 218235 - 239
326ILEILEALAALA(chain 'C' and (resid 9 through 54 or resid 56...CC221 - 235242 - 256
327GLUGLUILEILE(chain 'C' and (resid 9 through 54 or resid 56...CC238 - 264259 - 285
428ARGARGALAALA(chain 'D' and (resid 9 through 54 or resid 56...DD9 - 5330 - 74
429LEULEULEULEU(chain 'D' and (resid 9 through 54 or resid 56...DD5677
430ASNASNGLNGLN(chain 'D' and (resid 9 through 54 or resid 56...DD59 - 7280 - 93
431ALAALALYSLYS(chain 'D' and (resid 9 through 54 or resid 56...DD75 - 10896 - 129
432LEULEUPHEPHE(chain 'D' and (resid 9 through 54 or resid 56...DD111 - 190132 - 211
433GLUGLUMETMET(chain 'D' and (resid 9 through 54 or resid 56...DD208 - 211229 - 232
434VALVALLYSLYS(chain 'D' and (resid 9 through 54 or resid 56...DD214 - 218235 - 239
435ILEILEALAALA(chain 'D' and (resid 9 through 54 or resid 56...DD221 - 235242 - 256
436GLUGLUILEILE(chain 'D' and (resid 9 through 54 or resid 56...DD238 - 264259 - 285

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Components

#1: Protein
Borneol Dehydrogenase (salvia rosmarinus) apo structure


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 (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.0M NaCl 0.1M bis-tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25633 / % possible obs: 99.9 % / Redundancy: 25.9 % / Biso Wilson estimate: 82.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.194 / Rrim(I) all: 0.198 / Net I/σ(I): 16.49
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 25.4 % / Rmerge(I) obs: 2.125 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4012 / CC1/2: 0.889 / Rrim(I) all: 2.169 / % possible all: 99.6

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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: 3.1→50 Å / SU ML: 0.4793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3054 1280 5.01 %
Rwork0.2547 24276 -
obs0.2571 25556 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.81 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 0 3 7293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047383
X-RAY DIFFRACTIONf_angle_d0.74829993
X-RAY DIFFRACTIONf_chiral_restr0.04691213
X-RAY DIFFRACTIONf_plane_restr0.00391280
X-RAY DIFFRACTIONf_dihedral_angle_d12.32451049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.45141350.37172589X-RAY DIFFRACTION98.62
3.22-3.370.37381400.35082642X-RAY DIFFRACTION99.32
3.37-3.550.37891400.31472651X-RAY DIFFRACTION99.86
3.55-3.770.37381400.29212644X-RAY DIFFRACTION99.61
3.77-4.060.37081410.29052684X-RAY DIFFRACTION99.79
4.06-4.470.31361420.26032687X-RAY DIFFRACTION99.86
4.47-5.110.29761430.25812716X-RAY DIFFRACTION99.79
5.11-6.440.2881450.2572754X-RAY DIFFRACTION100
6.44-48.960.23331540.19112909X-RAY DIFFRACTION99.74

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