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- PDB-1ujm: Crystal structure of aldehyde reductase 2 from Sporobolomyces sal... -

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Basic information

Entry
Database: PDB / ID: 1ujm
TitleCrystal structure of aldehyde reductase 2 from Sporobolomyces salmonicolor AKU4429
ComponentsAldehyde reductase II
KeywordsOXIDOREDUCTASE / NADPH-dependent enzyme
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde reductase 2
Similarity search - Component
Biological speciesSporidiobolus salmonicolor (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKamitori, S. / Iguchi, A. / Ohtaki, A. / Kita, K.
CitationJournal: To be Published
Title: Crystal structure of aldehyde reductase 2 from Sporobolomyces salmonicolor AKU4429 at 2.0 A resolution
Authors: Kamitori, S. / Iguchi, A. / Ohtaki, A. / Kita, K.
History
DepositionAug 6, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde reductase II
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,88012
Polymers74,9192
Non-polymers96110
Water11,692649
1
A: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8445
Polymers37,4601
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0367
Polymers37,4601
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.869, 83.511, 148.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldehyde reductase II / aldehyde reductase 2 / ARII


Mass: 37459.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporidiobolus salmonicolor (yeast) / Strain: AKU4429 / Plasmid: pUC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG MME 2000, 0.1M Na Acetate, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97899, 0.97916, 1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979161
311
ReflectionResolution: 2→39.03 Å / Num. all: 47081 / Num. obs: 47081 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.055 / Net I/σ(I): 8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 6.3 / Num. unique all: 6783 / Rsym value: 0.096 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→39.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2323120.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4727 10.1 %RANDOM
Rwork0.198 ---
all0.203 47081 --
obs0.198 47013 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1516 Å2 / ksol: 0.359713 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.41 Å20 Å20 Å2
2---1.61 Å20 Å2
3----4.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 50 649 5959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 770 10 %
Rwork0.202 6958 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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