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- PDB-1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP -

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Basic information

Entry
Database: PDB / ID: 1ae1
TitleTROPINONE REDUCTASE-I COMPLEX WITH NADP
ComponentsTROPINONE REDUCTASE-ITropinone reductase II
KeywordsOXIDOREDUCTASE / TROPANE ALKALOID BIOSYNTHESIS / REDUCTION OF TROPINONE TO TROPINE / SHORT-CHAIN DEHYDROGENASE
Function / homology
Function and homology information


tropinone reductase I / tropine dehydrogenase activity / tropane alkaloid biosynthetic process
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Tropinone reductase 1
Similarity search - Component
Biological speciesDatura stramonium (jimsonweed)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 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 23, 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: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: TROPINONE REDUCTASE-I
B: TROPINONE REDUCTASE-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7834
Polymers59,2962
Non-polymers1,4872
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-22 kcal/mol
Surface area20470 Å2
MethodPISA
2
A: TROPINONE REDUCTASE-I
B: TROPINONE REDUCTASE-I
hetero molecules

A: TROPINONE REDUCTASE-I
B: TROPINONE REDUCTASE-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5658
Polymers118,5924
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area18960 Å2
ΔGint-115 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.740, 122.750, 75.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.91541, -0.40251, -0.00062), (-0.40251, 0.91541, 0.00293), (-0.00062, 0.00293, -1)102.79146, 21.50608, 62.06306
2given(-0.91541, -0.40251, -0.00062), (-0.40251, 0.91541, 0.00293), (-0.00062, 0.00293, -1)102.79146, 21.50608, 62.06306

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Components

#1: Protein TROPINONE REDUCTASE-I / Tropinone reductase II


Mass: 29647.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Datura stramonium (jimsonweed) / Cell line: BL21 / Organ: CULTURED ROOT / Plasmid: PETTR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P50162, tropinone reductase II
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.18 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.5 / Details: pH 4.5
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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 22, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→122.5 Å / Num. obs: 19708 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.48
Reflection shellResolution: 2.38→2.5 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.5 / % possible all: 83.6
Reflection
*PLUS
Num. measured all: 65888

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 928 5 %RANDOM
Rwork0.155 ---
obs0.155 19071 89.4 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 96 98 4041
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_deg0.974
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.73
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.72
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: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.294 93 5 %
Rwork0.193 2049 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 18143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.73
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.72

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