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- PDB-1k2w: Crystal structure of sorbitol dehydrogenase from R. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 1k2w
TitleCrystal structure of sorbitol dehydrogenase from R. sphaeroides
ComponentsSORBITOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase / enzyme
Function / homology
Function and homology information


galactitol 2-dehydrogenase activity / galactitol 2-dehydrogenase / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
PKS_KR / 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
Sorbitol dehydrogenase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPhilippsen, A. / Schirmer, T. / Stetefeld, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.
Authors: Philippsen, A. / Schirmer, T. / Stein, M.A. / Giffhorn, F. / Stetefeld, J.
#1: Journal: Microbiology (Reading, Engl.) / Year: 1995
Title: Polyol metabolism of Rhodobacter sphaeroides: biochemical characterization of a short-chain sorbitol dehydrogenase
Authors: Schauder, S. / Schneider, K.H. / Giffhorn, F.
History
DepositionSep 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SORBITOL DEHYDROGENASE
B: SORBITOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)54,0822
Polymers54,0822
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-18 kcal/mol
Surface area21350 Å2
MethodPISA
2
A: SORBITOL DEHYDROGENASE
B: SORBITOL DEHYDROGENASE

A: SORBITOL DEHYDROGENASE
B: SORBITOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)108,1634
Polymers108,1634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area12650 Å2
ΔGint-79 kcal/mol
Surface area36240 Å2
MethodPISA
3
A: SORBITOL DEHYDROGENASE

B: SORBITOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)54,0822
Polymers54,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2960 Å2
ΔGint-17 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.465, 67.465, 191.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsbiological assembly is dimer according to sedimentation analysis

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Components

#1: Protein SORBITOL DEHYDROGENASE / L-iditol 2-dehydrogenase / Polyol dehydrogenase


Mass: 27040.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59787, L-iditol 2-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.29 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMMES1reservoirpH7.0
318-21 %PEG40001reservoir
46-11 %methanol1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 22993 / Num. obs: 21038 / % possible obs: 91.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.079 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / % possible all: 73.3
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 2.57 Å / % possible obs: 92.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1GEG

1geg


Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1901 10 %RANDOM
Rwork0.188 ---
all-19115 --
obs-17214 --
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 0 170 3960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005871
X-RAY DIFFRACTIONc_angle_deg1.14081
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.14

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