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- PDB-1pz0: Structure of NADPH-dependent family 11 aldo-keto reductase AKR11A... -

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Basic information

Entry
Database: PDB / ID: 1pz0
TitleStructure of NADPH-dependent family 11 aldo-keto reductase AKR11A(holo)
ComponentsIolS protein
KeywordsOXIDOREDUCTASE / beta-alpha barrel / aldo-keto reductase / TIM barrel
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / cytosol
Similarity search - Function
: / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase IolS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsEhrensberger, A.H. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and Catalytic Diversity in the Two Family 11 Aldo-keto Reductases
Authors: Ehrensberger, A.H. / Wilson, D.K.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: IolS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2783
Polymers35,5121
Non-polymers7662
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.525, 84.262, 93.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne monomer forms the biological unit.

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Components

#1: Protein IolS protein / Vegetative protein 147 / VEG147


Mass: 35511.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: IOLS OR SS92ER / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P46336
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.37
Details: PEG 3000, NADP+, pH 10.37, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 10.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.9 mg/mlprotein1drop
25 mMNADP+1drop
340 %PEG30001reservoirpH10.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2003 / Details: Curved crystal
RadiationMonochromator: Curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. all: 14791 / Num. obs: 13331 / % possible obs: 90.13 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 17
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.3 / % possible all: 96.1
Reflection
*PLUS
Num. obs: 14813 / % possible obs: 94.3 % / Num. measured all: 45409
Reflection shell
*PLUS
% possible obs: 96.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AKR11A(apo)

Resolution: 2.35→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 678 -RANDOM
Rwork0.189 ---
all0.189 13309 --
obs0.189 13309 85.2 %-
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 49 210 2747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.35→2.43 Å / % reflection obs: 96.1 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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