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- PDB-1ynp: aldo-keto reductase AKR11C1 from Bacillus halodurans (apo form) -

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Basic information

Entry
Database: PDB / ID: 1ynp
Titlealdo-keto reductase AKR11C1 from Bacillus halodurans (apo 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 / Oxidoreductase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.25 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 30, 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)73,81817
Polymers72,2082
Non-polymers1,61015
Water10,557586
1
A: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33012
Polymers36,1041
Non-polymers1,22611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4885
Polymers36,1041
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.669, 86.566, 105.427
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)

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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 , 4 types, 600 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.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97784, 1.3783
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.977841
21.37831
ReflectionResolution: 1.25→38.71 Å / Num. all: 178042 / Num. obs: 178042 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 10
Reflection shellResolution: 1.25→1.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.7 / Num. unique all: 17279 / Rsym value: 0.506 / % possible all: 83.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.401data extraction
MAR345data collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.25→67.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.499 / SU ML: 0.029 / SU R Cruickshank DPI: 0.047 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.20584 8920 5 %RANDOM
Rwork0.17037 ---
obs0.17211 169110 94.43 %-
all-178030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--1.04 Å20 Å2
3----0.95 Å2
Refine analyzeLuzzati coordinate error free: 0.048 Å
Refinement stepCycle: LAST / Resolution: 1.25→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 90 586 5337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224849
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9926555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23423.891239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70215887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2381544
X-RAY DIFFRACTIONr_chiral_restr0.1050.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023601
X-RAY DIFFRACTIONr_nbd_refined0.2280.22348
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2465
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.232
X-RAY DIFFRACTIONr_mcbond_it2.72922887
X-RAY DIFFRACTIONr_mcangle_it3.72334657
X-RAY DIFFRACTIONr_scbond_it5.0654.52012
X-RAY DIFFRACTIONr_scangle_it6.79461897
X-RAY DIFFRACTIONr_rigid_bond_restr3.14134899
X-RAY DIFFRACTIONr_sphericity_free9.1463587
X-RAY DIFFRACTIONr_sphericity_bonded6.5334781
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 606 -
Rwork0.257 10782 -
obs--82.57 %

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