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- PDB-2glx: Crystal Structure Analysis of bacterial 1,5-AF Reductase -

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Basic information

Entry
Database: PDB / ID: 2glx
TitleCrystal Structure Analysis of bacterial 1,5-AF Reductase
Components1,5-anhydro-D-fructose reductase
KeywordsOXIDOREDUCTASE / NADP(H) dependent reductase / Rossmann-fold / bacterial 1 / 5-anhydro-D-fructose reductase / sugar metabolism / 1 / 5-anhydro-D-fructose / 5-anhydro-D-mannitol
Function / homology
Function and homology information


1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming) / 1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming) activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-NDP / 1,5-anhydro-D-fructose reductase
Similarity search - Component
Biological speciesEnsifer adhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDambe, T.R. / Scheidig, A.J.
Citation
Journal: Biochemistry / Year: 2006
Title: Crystal Structure of NADP(H)-Dependent 1,5-Anhydro-d-fructose Reductase from Sinorhizobium morelense at 2.2 A Resolution: Construction of a NADH-Accepting Mutant and Its Application in Rare Sugar Synthesis
Authors: Dambe, T.R. / Kuehn, A.M. / Brossette, T. / Giffhorn, F. / Scheidig, A.J.
#1: Journal: Appl.Environ.Microbiol. / Year: 2006
Title: Catabolism of 1,5-anhydro-D-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-D-fructose reductase and its application in sugar ...Title: Catabolism of 1,5-anhydro-D-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-D-fructose reductase and its application in sugar analysis and rare sugar synthesis
Authors: Kuehn, A.M. / Yu, S. / Giffhorn, F.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,5-anhydro-D-fructose reductase
B: 1,5-anhydro-D-fructose reductase
C: 1,5-anhydro-D-fructose reductase
D: 1,5-anhydro-D-fructose reductase
E: 1,5-anhydro-D-fructose reductase
F: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,67818
Polymers209,8516
Non-polymers4,82712
Water23,4921304
1
A: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7803
Polymers34,9751
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.190, 84.900, 150.940
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
1,5-anhydro-D-fructose reductase / / 1 / 5-AF-Reductase


Mass: 34975.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ensifer adhaerens (bacteria) / Strain: S-30.7.5 / Gene: afr / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2I8V6, EC: 1.1.1.263
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM NaCitrat, 200mM Ammoniumacetat, 30% MPEG 5000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.9788
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDApr 20, 2004
ADSC QUANTUM 42CCDMay 14, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorSINGLE WAVELENGTHMx-ray1
2mirrorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9331
ReflectionResolution: 2.2→19 Å / Num. all: 123108 / Num. obs: 123108 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 38.236 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 8.56
Reflection shellResolution: 2.2→2.3 Å / % possible obs: 96.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.6 / Num. measured obs: 52622 / Num. unique all: 15426 / Num. unique obs: 14875 / Rsym value: 0.448 / % possible all: 0.99

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
ProDCdata collection
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.687 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 6155 5 %RANDOM
Rwork0.19 ---
all0.193 123085 --
obs0.193 123085 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.652 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å2-2.28 Å2
2--2.47 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14736 0 312 1304 16352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02115324
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.96620868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0151986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40623.611648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.099152334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.08815120
X-RAY DIFFRACTIONr_chiral_restr0.130.22394
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211622
X-RAY DIFFRACTIONr_nbd_refined0.2690.27665
X-RAY DIFFRACTIONr_nbtor_refined0.3240.210312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.21328
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2182
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.243
X-RAY DIFFRACTIONr_mcbond_it2.8541.510017
X-RAY DIFFRACTIONr_mcangle_it3.69215594
X-RAY DIFFRACTIONr_scbond_it5.97935898
X-RAY DIFFRACTIONr_scangle_it7.9424.55274
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 452 -
Rwork0.26 8581 -
obs-9033 100 %

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