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- PDB-2ae1: TROPINONE REDUCTASE-II -

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Basic information

Entry
Database: PDB / ID: 2ae1
TitleTROPINONE REDUCTASE-II
ComponentsTROPINONE 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
Tropinone reductase 2
Similarity search - Component
Biological speciesDatura stramonium (jimsonweed)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsNakajima, K. / Yamashita, A. / Akama, H. / Nakatsu, T. / Kato, H. / Hashimoto, T. / Oda, J. / Yamada, Y.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Two Tropinone Reductases with Different Stereospecificities are Short-Chain Dehydrogenases Evolved from a Common Ancestor
Authors: Nakajima, K. / Hashimoto, T. / Yamada, Y.
History
DepositionOct 27, 1997Processing site: BNL
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TROPINONE REDUCTASE-II


Theoretical massNumber of molelcules
Total (without water)28,3391
Polymers28,3391
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TROPINONE REDUCTASE-II

A: TROPINONE REDUCTASE-II

A: TROPINONE REDUCTASE-II

A: TROPINONE REDUCTASE-II


Theoretical massNumber of molelcules
Total (without water)113,3584
Polymers113,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_667-y+1,-x+1,-z+21
Buried area15120 Å2
ΔGint-117 kcal/mol
Surface area32590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.800, 62.800, 128.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein TROPINONE REDUCTASE-II


Mass: 28339.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Datura stramonium (jimsonweed) / Cell line: BL21 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
25 mMTris-HCl1drop
38 mMNADP+1drop
42 mMdithiothreitol1drop
550 mMsodium citrate1reservoir
616-20 %(v/v)PEG10001reservoir
70.18-0.20 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 7, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→64.2 Å / Num. obs: 14339 / % possible obs: 81.8 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.65
Reflection shellResolution: 2.02→2.25 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.81 / % possible all: 55
Reflection
*PLUS
Num. measured all: 103356

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
PHASESphasing
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.306 628 6 %RANDOM
Rwork0.205 ---
obs0.205 10999 92.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.383 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.461 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 0 103 2025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.344 63 6 %
Rwork0.251 1047 -
obs--76.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
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_deg23.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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