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- PDB-8b1v: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga -

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Basic information

Entry
Database: PDB / ID: 8b1v
TitleDihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga
ComponentsDihydroprecondylocarpine acetate synthase 2
KeywordsCYTOSOLIC PROTEIN / Alcohol dehydrogenase
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / metal ion binding
Similarity search - Function
: / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
precondylocarpine acetate / Dihydroprecondylocarpine acetate synthase 2
Similarity search - Component
Biological speciesTabernanthe iboga (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.882 Å
AuthorsLangley, C. / Basquin, J. / Caputi, L. / O'Connor, S.E.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)788301European Union
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism.
Authors: Langley, C. / Tatsis, E. / Hong, B. / Nakamura, Y. / Paetz, C. / Stevenson, C.E.M. / Basquin, J. / Lawson, D.M. / Caputi, L. / O'Connor, S.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroprecondylocarpine acetate synthase 2
B: Dihydroprecondylocarpine acetate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4826
Polymers78,5602
Non-polymers9224
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-18 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.888, 79.624, 130.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 12 or (resid 13...
d_2ens_1(chain "B" and (resid 5 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROA1 - 358
d_12ens_1PCOPCOB
d_21ens_1SERPROC1 - 358
d_22ens_1PCOPCOD

NCS oper: (Code: givenMatrix: (-0.999927984975, -9.47613017704E-5, -0.0120006617997), (-0.00105857201491, 0.996767576052, 0.0803323020716), (0.0119542581796, 0.0803392205036, -0.996695894122)Vector: ...NCS oper: (Code: given
Matrix: (-0.999927984975, -9.47613017704E-5, -0.0120006617997), (-0.00105857201491, 0.996767576052, 0.0803323020716), (0.0119542581796, 0.0803392205036, -0.996695894122)
Vector: 109.884874539, -7.73614508623, 187.946300156)

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Components

#1: Protein Dihydroprecondylocarpine acetate synthase 2


Mass: 39280.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tabernanthe iboga (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B8X8Z0
#2: Chemical ChemComp-ORZ / precondylocarpine acetate / methyl (1~{S},2~{S},16~{E})-2-(acetyloxymethyl)-16-ethylidene-4-aza-14-azoniatetracyclo[12.2.2.0^{3,11}.0^{5,10}]octadeca-3(11),5(10),6,8,14-pentaene-2-carboxylate


Mass: 395.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 17% w/v PEG 3350, 200 mM ammonium chloride and 0.75 mM angryline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.882→39.81 Å / Num. obs: 62174 / % possible obs: 99.49 % / Redundancy: 13 % / Biso Wilson estimate: 40.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.05
Reflection shellResolution: 1.882→1.949 Å / Num. unique obs: 5895 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FI3

5fi3


Resolution: 1.882→39.81 Å / SU ML: 0.3374 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 5905 4.98 %
Rwork0.2019 112781 -
obs0.2029 62174 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.14 Å2
Refinement stepCycle: LAST / Resolution: 1.882→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 60 246 5578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365447
X-RAY DIFFRACTIONf_angle_d0.77787432
X-RAY DIFFRACTIONf_chiral_restr0.0525876
X-RAY DIFFRACTIONf_plane_restr0.0067952
X-RAY DIFFRACTIONf_dihedral_angle_d5.5832764
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.519948193521 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.882-1.90.75571750.60133309X-RAY DIFFRACTION87.14
1.9-1.930.50321960.47083806X-RAY DIFFRACTION99.9
1.93-1.950.44481940.43443719X-RAY DIFFRACTION99.87
1.95-1.970.41732020.39343807X-RAY DIFFRACTION99.85
1.97-20.3651950.34783753X-RAY DIFFRACTION99.9
2-2.030.32321980.32023768X-RAY DIFFRACTION99.9
2.03-2.060.29621980.29623752X-RAY DIFFRACTION99.97
2.06-2.090.32271990.28383820X-RAY DIFFRACTION99.98
2.09-2.120.27661950.27623745X-RAY DIFFRACTION99.82
2.12-2.150.31871970.27263809X-RAY DIFFRACTION100
2.15-2.190.29142000.26673755X-RAY DIFFRACTION99.87
2.19-2.230.26311960.26413765X-RAY DIFFRACTION99.97
2.23-2.270.27022000.24193840X-RAY DIFFRACTION99.95
2.27-2.320.27111920.22953690X-RAY DIFFRACTION99.95
2.32-2.370.32711890.2293787X-RAY DIFFRACTION100
2.37-2.430.31542040.2273838X-RAY DIFFRACTION99.98
2.43-2.490.24741940.21373714X-RAY DIFFRACTION99.9
2.49-2.550.23752050.22083805X-RAY DIFFRACTION100
2.55-2.630.25511980.21493782X-RAY DIFFRACTION100
2.63-2.710.23661970.21793771X-RAY DIFFRACTION99.92
2.71-2.810.29611960.21423768X-RAY DIFFRACTION99.97
2.81-2.920.26232030.21873788X-RAY DIFFRACTION99.87
2.92-3.060.22061960.20413771X-RAY DIFFRACTION99.95
3.06-3.220.2382030.21143759X-RAY DIFFRACTION99.97
3.22-3.420.22311940.19273780X-RAY DIFFRACTION99.9
3.42-3.680.18411980.17413774X-RAY DIFFRACTION100
3.68-4.050.16751960.16113799X-RAY DIFFRACTION100
4.05-4.640.16582010.14793754X-RAY DIFFRACTION99.92
4.64-5.840.1611930.15833776X-RAY DIFFRACTION99.97
5.84-39.810.16642010.17693777X-RAY DIFFRACTION99.67

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