[English] 日本語
Yorodumi
- PDB-1cyd: CARBONYL REDUCTASE COMPLEXED WITH NADPH AND 2-PROPANOL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cyd
TitleCARBONYL REDUCTASE COMPLEXED WITH NADPH AND 2-PROPANOL
ComponentsCARBONYL REDUCTASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE
Function / homology
Function and homology information


L-xylulose reductase (NADPH) activity / xylulose metabolic process / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / NADH oxidation / glucose metabolic process / : / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
short chain dehydrogenase / 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
ISOPROPYL ALCOHOL / Chem-NDP / Carbonyl reductase [NADPH] 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTanaka, N. / Nonaka, T. / Mitsui, Y.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 A resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family.
Authors: Tanaka, N. / Nonaka, T. / Nakanishi, M. / Deyashiki, Y. / Hara, A. / Mitsui, Y.
#1: Journal: To be Published
Title: Crystallization of Mouse Lung Carbonyl Reductase Complexed with Nadph and Analysis of Symmetry of its Tetrameric Molecule
Authors: Tanaka, N. / Nonaka, T. / Nakanishi, M. / Deyashiki, Y. / Hara, A. / Mitsui, Y.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: Cloning, Expression and Tissue Distribution of Mouse Tetrameric Carbonyl Reductase. Identity with an Adipocyte 27-kDa Protein
Authors: Nakanishi, M. / Deyashiki, Y. / Ohshima, K. / Hara, A.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 4, 2013Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: CARBONYL REDUCTASE
B: CARBONYL REDUCTASE
C: CARBONYL REDUCTASE
D: CARBONYL REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,17912
Polymers103,9574
Non-polymers3,2228
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-80 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.730, 105.500, 60.870
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.40641, 0.912979, -0.036055), (0.913238, -0.407134, -0.015429), (-0.028786, -0.026656, -0.999231)11.7812, -17.0202, 33.2416
2given(-1, 0.000319, -0.000173), (-0.00033, -0.997311, 0.073285), (-0.000149, 0.073285, 0.997311)38.4974, -0.7571, 0.0132
3given(-0.406457, -0.91301, 0.034729), (-0.913232, 0.404792, -0.046373), (0.028281, -0.050564, -0.99832)26.6433, 18.4725, 32.1171

-
Components

#1: Protein
CARBONYL REDUCTASE


Mass: 25989.178 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THIS PROTEIN IS IDENTICAL WITH AN ADIPOCYTE 27-KDA PROTEIN
Source: (natural) Mus musculus (house mouse) / Cell: EPITHELIAL CELL / Organ: LUNG / Organelle: MITOCHONDRION / Strain: DDY MICE / Tissue: EPITHELIAL / References: UniProt: P08074, carbonyl reductase (NADPH)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlMLCR1drop
2200 mM1dropNaCl
32 mg/mlNADPH1drop
420 mMTris1drop
517 %(w/v)PEG40001reservoir
6200 mM1reservoirNaOAc
79 %(v/v)2-propanol1reservoir
8100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 3, 1994 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→79.1 Å / Num. obs: 67478 / % possible obs: 72.4 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Lowest resolution: 79 Å / Num. measured all: 224849
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 49.7 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.202 -10 %
Rwork0.154 --
obs0.154 66795 72.2 %
Displacement parametersBiso mean: 14.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7200 0 208 580 7988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.515
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d20
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

+
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