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- PDB-3afn: Crystal structure of aldose reductase A1-R complexed with NADP -

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Basic information

Entry
Database: PDB / ID: 3afn
TitleCrystal structure of aldose reductase A1-R complexed with NADP
ComponentsCarbonyl reductase
KeywordsOXIDOREDUCTASE / ALPHA/BETA/ALPHA / ROSSMANN-FOLD
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / PKS_KR / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TERTIARY-BUTYL ALCOHOL / Carbonyl reductase
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsTakase, R. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1
Authors: Takase, R. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionMar 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Carbonyl reductase
A: Carbonyl reductase
C: Carbonyl reductase
D: Carbonyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,19212
Polymers107,9224
Non-polymers3,2708
Water16,700927
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-73 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.404, 64.195, 74.441
Angle α, β, γ (deg.)80.15, 66.08, 64.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Carbonyl reductase / A1-R / 4-deoxy-L-erythro-5-hexoseulose-uronic acid reductase


Mass: 26980.525 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: A1 / Gene: a1-R / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6RU56, EC: 1.1.1.126
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 47% 2-methyl-2,4-pentanediol, 2% tert-butanol, 0.5mM NADP, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 19, 2008
RadiationMonochromator: Si(111) double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 115155 / % possible obs: 95.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 19.7
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 3.82 / % possible all: 88.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFM

3afm


Resolution: 1.63→22.68 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.892 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20858 5537 5 %RANDOM
Rwork0.1723 ---
obs0.17411 104849 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.711 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7568 0 212 927 8707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228176
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.97411130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.92951072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0823.574333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.901151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7521547
X-RAY DIFFRACTIONr_chiral_restr0.070.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026267
X-RAY DIFFRACTIONr_nbd_refined0.1880.24376
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2873
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.223
X-RAY DIFFRACTIONr_mcbond_it0.4491.55354
X-RAY DIFFRACTIONr_mcangle_it0.7728256
X-RAY DIFFRACTIONr_scbond_it1.09233182
X-RAY DIFFRACTIONr_scangle_it1.6534.52873
LS refinement shellResolution: 1.632→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 385 -
Rwork0.269 6945 -
obs--86.23 %

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