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- PDB-1dla: NOVEL NADPH-BINDING DOMAIN REVEALED BY THE CRYSTAL STRUCTURE OF A... -

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Basic information

Entry
Database: PDB / ID: 1dla
TitleNOVEL NADPH-BINDING DOMAIN REVEALED BY THE CRYSTAL STRUCTURE OF ALDOSE REDUCTASE
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE(NADP)
Function / homology
Function and homology information


aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity ...aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / retinoid metabolic process / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsRondeau, J.-M. / Tete-Favier, F. / Podjarny, A. / Reymann, J.-M. / Barth, P. / Biellmann, J.-F. / Moras, D.
Citation
Journal: Nature / Year: 1992
Title: Novel NADPH-binding domain revealed by the crystal structure of aldose reductase.
Authors: Rondeau, J.M. / Tete-Favier, F. / Podjarny, A. / Reymann, J.M. / Barth, P. / Biellmann, J.F. / Moras, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure Determination of Aldose Reductase: Joys and Traps of Local Symmetry Averaging
Authors: Tete-Favier, F. / Rondeau, J.-M. / Podjarny, A. / Moras, D.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary X-Ray Study of Pig Lens Aldose Reductase
Authors: Rondeau, J.-M. / Samama, J.-P. / Samama, B. / Barth, P. / Moras, D. / Biellmann, J.-F.
History
DepositionFeb 8, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *BRA*, *BRB*, *BRC*, AND *BRD* ON SHEET RECORDS BELOW ARE ACTUALLY ...SHEET THE SHEETS PRESENTED AS *BRA*, *BRB*, *BRC*, AND *BRD* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDOSE REDUCTASE
B: ALDOSE REDUCTASE
C: ALDOSE REDUCTASE
D: ALDOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)142,8444
Polymers142,8444
Non-polymers00
Water00
1
A: ALDOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)35,7111
Polymers35,7111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALDOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)35,7111
Polymers35,7111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ALDOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)35,7111
Polymers35,7111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ALDOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)35,7111
Polymers35,7111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.300, 85.900, 56.600
Angle α, β, γ (deg.)102.30, 103.30, 79.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.45654, 0.05706, 0.88787), (0.08505, -0.99617, 0.02026), (0.88562, 0.06628, -0.45965)-0.24, -1.13, -0.18
2given(-0.88362, -0.39806, -0.24652), (-0.45998, 0.63984, 0.61566), (-0.08733, 0.65739, -0.74847)-1.7, 0.32, 0.65
3given(-0.61888, 0.38763, -0.68318), (0.34043, -0.65146, -0.67801), (-0.70789, -0.65218, 0.27122)-0.58, -1.12, -1.37
4given(-0.64498, 0.31637, -0.69565), (0.37305, -0.66412, -0.64791), (-0.66697, -0.67739, 0.31032)-1.62, -0.46, -0.21
5given(-0.86705, -0.45256, -0.20839), (-0.48368, 0.66429, 0.56988), (-0.11947, 0.5949, -0.79487)-1.33, -0.38, -0.87
6given(0.559845, 0.120104, 0.819847), (0.110852, -0.991401, 0.069539), (0.821149, 0.051951, -0.568345)-0.38433, -0.68345, 0.92487

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Components

#1: Protein
ALDOSE REDUCTASE / Coordinate model: Cα atoms only


Mass: 35710.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P80276, aldose reductase
Sequence detailsSEQUENCE ADVISORY NOTICE: SEQUENCE NOT IN SWISS-PROT DATA BASE. THE SEQUENCE PRESENTED BELOW IS ...SEQUENCE ADVISORY NOTICE: SEQUENCE NOT IN SWISS-PROT DATA BASE. THE SEQUENCE PRESENTED BELOW IS THAT DESCRIBED BY M. JAQUINOD ET AL.,( EUR. J. BIOCHEM. 218, 893, 1993).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlenzyme1drop
22.5 %(w/v)PEG60001drop
310 mMcitrate1drop
41 mMdithiothreitol1drop
51 mMsodium azide1drop
620 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 82 Å / Num. obs: 40833 / % possible obs: 82 % / Num. measured all: 128597 / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.219 / Rfactor obs: 0.219 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 0 1242
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.7
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_deg1.6

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