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- PDB-3ai2: The crystal structure of L-sorbose reductase from Gluconobacter f... -

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Basic information

Entry
Database: PDB / ID: 3ai2
TitleThe crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH
ComponentsNADPH-sorbose reductase
KeywordsOXIDOREDUCTASE / Rossmann-fold / NADPH-dependent reductase / short chain dehydrogenase/reductase
Function / homology
Function and homology information


monocarboxylic acid metabolic process / lipid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NADPH-sorbose reductase
Similarity search - Component
Biological speciesGluconobacter frateurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Tanokura, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose
Authors: Kubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Soemphol, W. / Ohtsuka, J. / Yamamura, A. / Saichana, N. / Toyama, H. / Matsushita, K. / Tanokura, M.
History
DepositionMay 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Nov 1, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: NADPH-sorbose reductase
B: NADPH-sorbose reductase
H: NADPH-sorbose reductase
D: NADPH-sorbose reductase
E: NADPH-sorbose reductase
C: NADPH-sorbose reductase
F: NADPH-sorbose reductase
G: NADPH-sorbose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,77616
Polymers226,8128
Non-polymers5,9638
Water25,4191411
1
A: NADPH-sorbose reductase
B: NADPH-sorbose reductase
D: NADPH-sorbose reductase
C: NADPH-sorbose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3888
Polymers113,4064
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13410 Å2
ΔGint-107 kcal/mol
Surface area37090 Å2
MethodPISA
2
H: NADPH-sorbose reductase
E: NADPH-sorbose reductase
F: NADPH-sorbose reductase
G: NADPH-sorbose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3888
Polymers113,4064
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-106 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.290, 60.980, 124.450
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADPH-sorbose reductase / L-Sorbose Reductase


Mass: 28351.529 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter frateurii (bacteria) / Gene: sboA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A4PB64, EC: 1.1.1.289
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1411 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 5MM NADPH, 34% (W/V) PEG 400, 200MM CALCIUM ACETATE, 100MM SODIUM ACETATE TRIHYDRATE PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 146936 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AI1

3ai1


Resolution: 1.9→19.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.414 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.221 7364 5 %RANDOM
Rwork0.172 ---
obs0.175 139564 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15928 0 384 1411 17723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02216648
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9822632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91852096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99523.902656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.412152712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8421596
X-RAY DIFFRACTIONr_chiral_restr0.1160.22568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112320
X-RAY DIFFRACTIONr_mcbond_it0.9641.510384
X-RAY DIFFRACTIONr_mcangle_it1.653216600
X-RAY DIFFRACTIONr_scbond_it2.90736264
X-RAY DIFFRACTIONr_scangle_it4.7114.56032
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 510 -
Rwork0.215 10156 -
obs--99.81 %

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