[English] 日本語
Yorodumi
- PDB-1ipe: TROPINONE REDUCTASE-II COMPLEXED WITH NADPH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ipe
TitleTROPINONE REDUCTASE-II COMPLEXED WITH NADPH
ComponentsTROPINONE REDUCTASE-II
KeywordsOXIDOREDUCTASE / TROPANE ALKALOID BIOSYNTHESIS / REDUCTION OF TROPINONE TO PSEUDOTROPINE / SHORT-CHAIN DEHYDROGENASE / LAUE DIFFRACTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Chem-NDP / Tropinone reductase 2
Similarity search - Component
Biological speciesDatura stramonium (jimsonweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYamashita, A. / Endo, M. / Higashi, T. / Nakatsu, T. / Yamada, Y. / Oda, J. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: BIOCHEMISTRY / Year: 2003
Title: Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes
Authors: Yamashita, A. / Endo, M. / Higashi, T. / Nakatsu, T. / Yamada, Y. / Oda, J. / Kato, H.
#1: 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.
#2: 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
DepositionMay 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,9074
Polymers56,4172
Non-polymers1,4912
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-26 kcal/mol
Surface area20830 Å2
MethodPISA
2
A: TROPINONE REDUCTASE-II
B: TROPINONE REDUCTASE-II
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)115,8158
Polymers112,8334
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area20130 Å2
ΔGint-126 kcal/mol
Surface area31800 Å2
MethodPISA
3
A: TROPINONE REDUCTASE-II
hetero molecules

B: TROPINONE REDUCTASE-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9074
Polymers56,4172
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6100 Å2
ΔGint-33 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 88.600, 338.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

-
Components

#1: Protein TROPINONE REDUCTASE-II


Mass: 28208.250 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, dithiothreitol, HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal grow
*PLUS
Method: unknown
Details: Petsko, G.A., (2000) Curr. Opin. Chem. Biol., 4, 89.

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.7-1.65
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 11, 1998
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
21.651
ReflectionResolution: 2.5→43 Å / Num. all: 24884 / Num. obs: 24496 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 6.11 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.134
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.28 / % possible all: 82.8
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 149781
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.28

-
Processing

Software
NameVersionClassification
INTLAUEdata collection
LAUENORMdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
INTLAUEdata reduction
LAUENORMdata scaling
X-PLOR3.851phasing
RefinementStarting model: PDB ENTRY 2AE2

2ae2


Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: This solvent would make a 3.5 A hydrogen bond with HOH 26, which makes a hydrogen bond with protein molecule with 3.4 A distance.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1184 5 %RANDOM
Rwork0.195 ---
obs-23229 83.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 96 61 4107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d24.57
X-RAY DIFFRACTIONx_improper_angle_d0.67
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 124 3.63 %
Rwork0.256 2486 -
obs-2894 76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2NPH.PARAMTOPH19.SOL
X-RAY DIFFRACTION3NPH.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.302
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.569
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.669

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more