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- PDB-2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE -

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Basic information

Entry
Database: PDB / ID: 2ae2
TitleTROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE
ComponentsPROTEIN (TROPINONE REDUCTASE-II)
KeywordsOXIDOREDUCTASE / TROPANE ALKALOID BIOSYNTHESIS / REDUCTION OF TROPINONE TO PSEUDOTROPINE / SHORT-CHAIN DEHYDROGENASE
Function / homology
Function and homology information


tropinone reductase II / tropinone reductase activity / tropane alkaloid biosynthetic process
Similarity search - Function
Tropinone reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PSEUDOTROPINE / Tropinone reductase 2
Similarity search - Component
Biological speciesDatura stramonium (jimsonweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYamashita, A. / Kato, H. / Wakatsuki, S. / Tomizaki, T. / Nakatsu, T. / Nakajima, K. / Hashimoto, T. / Yamada, Y. / Oda, J.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.
Authors: Yamashita, A. / Kato, H. / Wakatsuki, S. / Tomizaki, T. / Nakatsu, T. / Nakajima, K. / Hashimoto, T. / Yamada, Y. / Oda, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structures of two tropinone reductases: different reaction stereospecificities in the same protein fold.
Authors: Nakajima, K. / Yamashita, A. / Akama, H. / Nakatsu, T. / Kato, H. / Hashimoto, T. / Oda, J. / Yamada, Y.
History
DepositionJan 26, 1999Processing site: RCSB
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (TROPINONE REDUCTASE-II)
B: PROTEIN (TROPINONE REDUCTASE-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4486
Polymers56,6792
Non-polymers1,7694
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-13 kcal/mol
Surface area20360 Å2
MethodPISA
2
A: PROTEIN (TROPINONE REDUCTASE-II)
B: PROTEIN (TROPINONE REDUCTASE-II)
hetero molecules

A: PROTEIN (TROPINONE REDUCTASE-II)
B: PROTEIN (TROPINONE REDUCTASE-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,89612
Polymers113,3584
Non-polymers3,5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area21870 Å2
ΔGint-99 kcal/mol
Surface area30810 Å2
MethodPISA
3
A: PROTEIN (TROPINONE REDUCTASE-II)
hetero molecules

B: PROTEIN (TROPINONE REDUCTASE-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4486
Polymers56,6792
Non-polymers1,7694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6920 Å2
ΔGint-20 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 88.600, 338.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.89137, 0.19074, -0.41118), (0.18739, -0.67093, -0.71745), (-0.41272, -0.71657, 0.56231)
Vector: 95.76153, 159.28313, 98.29375)

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Components

#1: Protein PROTEIN (TROPINONE REDUCTASE-II)


Mass: 28339.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Datura stramonium (jimsonweed) / Organ: CULTURED ROOT / Plasmid: PETTR2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P50163, tropinone reductase II
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-PTO / PSEUDOTROPINE


Mass: 141.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.42 Å3/Da / Density % sol: 64.1 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
24 mMNADP+1drop
320 mMphi-tropine1drop
45 mMTris-HCl1drop
51 mMdithiothreitol1drop
60.1 MHEPES1reservoir
71.7 M1reservoirLi2SO4
81 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.918
DetectorDetector: IMAGE PLATE / Date: Jul 13, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→64.2 Å / Num. obs: 54120 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.247 / % possible all: 77.9
Reflection
*PLUS
Num. measured all: 195899
Reflection shell
*PLUS
% possible obs: 77.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AE1

2ae1


Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2630 5 %RANDOM
Rwork0.172 ---
obs-51904 82.9 %-
Displacement parametersBiso mean: 19.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.212 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 116 236 4302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.275
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.83
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.806
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 300 3.91 %
Rwork0.247 5307 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2NAP_IN_1CYD.PARTOPH19.SOL
X-RAY DIFFRACTION3PARAM.PTONAP_IN_1CYD.TOP
X-RAY DIFFRACTION4TOPOLOGY.PTO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.83
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.806

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