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- PDB-3lqf: Crystal structure of the short-chain dehydrogenase Galactitol-Deh... -

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Basic information

Entry
Database: PDB / ID: 3lqf
TitleCrystal structure of the short-chain dehydrogenase Galactitol-Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD and erythritol
ComponentsGalactitol dehydrogenase
KeywordsOXIDOREDUCTASE / SDR / ROSSMANN FOLD / TAGATOSE / GALACTITOL
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
MESO-ERYTHRITOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Galactitol 2-dehydrogenase (L-tagatose-forming)
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCarius, Y. / Christian, H. / Faust, A. / Kornberger, P. / Zander, U. / Klink, B.U. / 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
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)108,82314
Polymers105,6334
Non-polymers3,19110
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21840 Å2
ΔGint-132 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.863, 113.838, 123.234
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) / 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-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100MM MES, 200MM MAGNESIUMCHLORIDE, 14.0%(W/V)MPEG5000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92
DetectorType: RAYONIX / Detector: CCD / Date: Oct 17, 2008 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 83822 / Num. obs: 83822 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.474 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.65
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.96 / Num. unique all: 6087 / Rsym value: 0.68 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS PROT MODEL

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.952 / SU ML: 0.092 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22267 4191 5 %RANDOM
Rwork0.18419 ---
all0.1861 79631 --
obs0.1861 79631 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: 24.924 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--2.36 Å20 Å2
3----1.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 210 509 8111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227732
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97910536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9651012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58322.192292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.112151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4871576
X-RAY DIFFRACTIONr_chiral_restr0.0930.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215812
X-RAY DIFFRACTIONr_mcbond_it0.7871.55016
X-RAY DIFFRACTIONr_mcangle_it1.33127888
X-RAY DIFFRACTIONr_scbond_it2.06232716
X-RAY DIFFRACTIONr_scangle_it3.244.52648
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 304 -
Rwork0.262 5783 -
obs-5783 100 %

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