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- PDB-2bgq: apo aldose reductase from barley -

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Basic information

Entry
Database: PDB / ID: 2bgq
Titleapo aldose reductase from barley
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE / ALDOSE REDUCTASE / APOENZYME / ALDO/KETO REDUCTASE OXIDOREDUCTASE
Function / homology
Function and homology information


aldose reductase / aldose reductase (NADPH) activity / oxidoreductase activity
Similarity search - Function
Aldo-keto reductase family 4C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 ...Aldo-keto reductase family 4C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Aldose reductase / Aldose reductase
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOlsen, J.G. / Pedersen, L. / Christensen, C.L. / Olsen, O. / Henriksen, A.
Citation
Journal: Proteins: Struct., Funct., Bioinf. / Year: 2008
Title: Barley Aldose Reductase: Structure, Cofactor Binding, and Substrate Recognition in the Aldo/Keto Reductase 4C Family.
Authors: Olsen, J.G. / Pedersen, L. / Christensen, C.L. / Olsen, O. / Henriksen, A.
#1: Journal: Embo J. / Year: 1991
Title: An Aba and Ga Modulated Gene Expressed in the Barley Embryo Encodes an Aldose Reductase Related Protein
Authors: Bartels, D. / Engelhardt, K. / Roncarati, R. / Schneider, K. / Rotter, M. / Salamini, F.
History
DepositionJan 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9432
Polymers38,8471
Non-polymers961
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.518, 69.180, 50.468
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALDOSE REDUCTASE / AR / ALDEHYDE REDUCTASE


Mass: 38847.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HORDEUM VULGARE (barley) / Strain: AURA / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q42837, UniProt: P23901*PLUS, aldose reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 25 RESIDUES IN THE SEQRES RECORDS GIVEN BELOW ARE FROM AN ENGINEERED N-TERMINAL HIS-TAG ...THE FIRST 25 RESIDUES IN THE SEQRES RECORDS GIVEN BELOW ARE FROM AN ENGINEERED N-TERMINAL HIS-TAG INCLUDING AN AN ENTEROKINASE CLEAVAGE SITE

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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: 2.21 Å3/Da / Density % sol: 43.87 % / Description: NONE
Crystal growpH: 6 / Details: 2.4 M (NH4)2SO4, 0.1 M MES PH 6.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 10, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23.6 Å / Num. obs: 15083 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 3.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADS

1ads


Resolution: 2.5→20.31 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1158983.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: NOT SIGNIFICANT ELECTRON DENSITY FOR RESIDUES 1-8, 33-36 AND 219-221, WHICH ARE OMITTED FROM THE COORDINATE LIST
RfactorNum. reflection% reflectionSelection details
Rfree0.249 526 5 %RANDOM
Rwork0.196 ---
obs0.196 10612 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9285 Å2 / ksol: 0.405236 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.33 Å2
2--6.8 Å20 Å2
3----6.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.5→20.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 5 183 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 90 5.1 %
Rwork0.221 1683 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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