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- PDB-1ynq: aldo-keto reductase AKR11C1 from Bacillus halodurans (holo form) -

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Basic information

Entry
Database: PDB / ID: 1ynq
Titlealdo-keto reductase AKR11C1 from Bacillus halodurans (holo form)
Componentsoxidoreductase
KeywordsOXIDOREDUCTASE / aldo-keto reductase / AKR11C1 / NADPH / Bacillus halodurans
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADP-dependent oxidoreductase domain / 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
sucrose / Chem-NDP / Oxidoreductase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous / Resolution: 1.3 Å
AuthorsMarquardt, T. / Kostrewa, D. / Winkler, F.K. / Li, X.D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: High-resolution Crystal Structure of AKR11C1 from Bacillus halodurans: An NADPH-dependent 4-Hydroxy-2,3-trans-nonenal Reductase
Authors: Marquardt, T. / Kostrewa, D. / Balakrishnan, R. / Gasperina, A. / Kambach, C. / Podjarny, A. / Winkler, F.K. / Balendiran, G.K. / Li, X.D.
History
DepositionJan 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidoreductase
B: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65119
Polymers72,2082
Non-polymers2,44417
Water12,304683
1
A: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,23811
Polymers36,1041
Non-polymers1,13410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4148
Polymers36,1041
Non-polymers1,3107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.122, 87.543, 105.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details2 biological units in the ASU (chain A and chain B). Chain B bound to NADPH.

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein oxidoreductase / AKR11C1


Mass: 36103.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH1011 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9KE47
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 699 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: (NH4)2SO4, Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.3→38.71 Å / Num. all: 169631 / Num. obs: 169631 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 9.38
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.5 / Num. unique all: 33318 / Rsym value: 0.506 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.401data extraction
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: isomorphous / Resolution: 1.3→67.42 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.409 / SU ML: 0.027 / SU R Cruickshank DPI: 0.045 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18534 8499 5 %RANDOM
Rwork0.15172 ---
obs0.15339 161130 99.36 %-
all-169629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.62 Å20 Å2
3----0.46 Å2
Refine analyzeLuzzati coordinate error free: 0.046 Å
Refinement stepCycle: LAST / Resolution: 1.3→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 145 683 5546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224957
X-RAY DIFFRACTIONr_angle_refined_deg1.7152.0016711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54123.817241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53315885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1341544
X-RAY DIFFRACTIONr_chiral_restr0.1030.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023668
X-RAY DIFFRACTIONr_nbd_refined0.2250.22312
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2528
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.247
X-RAY DIFFRACTIONr_mcbond_it2.45822910
X-RAY DIFFRACTIONr_mcangle_it3.53434689
X-RAY DIFFRACTIONr_scbond_it5.0724.52117
X-RAY DIFFRACTIONr_scangle_it6.62262022
X-RAY DIFFRACTIONr_rigid_bond_restr3.31235027
X-RAY DIFFRACTIONr_sphericity_free8.93684
X-RAY DIFFRACTIONr_sphericity_bonded6.14734880
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 625 -
Rwork0.204 11744 -
obs--98.96 %

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