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- PDB-2wsb: Crystal structure of the short-chain dehydrogenase Galactitol- De... -

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Basic information

Entry
Database: PDB / ID: 2wsb
TitleCrystal structure of the short-chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD
ComponentsGALACTITOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SDR / ROSSMANN FOLD / TAGATOSE
Function / homology
Function and homology information


galactitol 2-dehydrogenase (L-tagatose-forming) / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding
Similarity search - Function
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / N-PROPANOL / Galactitol 2-dehydrogenase (L-tagatose-forming)
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCarius, Y. / Christian, H. / Faust, A. / Kornberger, P. / Kohring, G.W. / Giffhorn, F. / Scheidig, A.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insight Into Substrate Differentiation of the Sugar-Metabolizing Enzyme Galactitol Dehydrogenase from Rhodobacter Sphaeroides D.
Authors: Carius, Y. / Christian, H. / Faust, A. / Zander, U. / Klink, B.U. / Kornberger, P. / Kohring, G.W. / Giffhorn, F. / Scheidig, A.J.
History
DepositionSep 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: GALACTITOL DEHYDROGENASE
B: GALACTITOL DEHYDROGENASE
C: GALACTITOL DEHYDROGENASE
D: GALACTITOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,81618
Polymers105,6334
Non-polymers3,18314
Water31,7961765
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22190 Å2
ΔGint-84.4 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.790, 106.620, 109.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GALACTITOL DEHYDROGENASE


Mass: 26408.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: D / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0KTJ6, galactitol 2-dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1765 / 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: 2.71 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5
Details: 4% N-PROPANOLE, 100MM SODIUM CACODYLATE, PH 6.5, 200MM SODIUM ACETATE, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.25→19.94 Å / Num. obs: 313700 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS PROT MODEL

Resolution: 1.25→19.94 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.548 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.041
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17749 15666 5 %RANDOM
Rwork0.13393 ---
obs0.13609 313320 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 210 1765 9367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0218361
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5811.97611442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31451135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9721.726336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.454151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.65415101
X-RAY DIFFRACTIONr_chiral_restr0.1680.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0216477
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.2125
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.11.55381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.11228548
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.86332980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.3784.52885
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.0718361
X-RAY DIFFRACTIONr_sphericity_free21.10751767
X-RAY DIFFRACTIONr_sphericity_bonded9.85158175
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 1145 -
Rwork0.284 21748 -
obs--99.66 %

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