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- PDB-1cyd: CARBONYL REDUCTASE COMPLEXED WITH NADPH AND 2-PROPANOL -

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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


carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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 %

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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

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