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

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Basic information

Entry
Database: PDB / ID: 2wdz
TitleCrystal structure of the short chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD+ and 1,2-Pentandiol
ComponentsSHORT-CHAIN DEHYDROGENASE/REDUCTASE
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
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
(2S)-pentane-1,2-diol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Galactitol 2-dehydrogenase (L-tagatose-forming) / Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionMar 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
C: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
D: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,90417
Polymers105,6334
Non-polymers3,27213
Water8,917495
1
A: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules

A: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,00818
Polymers105,6334
Non-polymers3,37614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area20450 Å2
ΔGint-140.8 kcal/mol
Surface area28530 Å2
MethodPISA
2
C: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
D: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules

C: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
D: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,80016
Polymers105,6334
Non-polymers3,16812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area22190 Å2
ΔGint-141.4 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.720, 113.620, 256.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-255-

MG

21B-255-

MG

31A-2145-

HOH

41A-2146-

HOH

51B-2114-

HOH

61B-2116-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.0043, 0.003), (0.0049, 0.9746, 0.2237), (0.003, 0.2237, -0.9746)12.7067, -0.0631, 0.0209
2given(-0.9144, 0.0008, -0.4048), (-0.0019, -1, 0.0024), (-0.4048, 0.0029, 0.9144)25.934, 99.4586, 5.3809

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Components

#1: Protein
SHORT-CHAIN DEHYDROGENASE/REDUCTASE / GALACTITOL 2-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: Q3J3W2, UniProt: C0KTJ6*PLUS, galactitol 2-dehydrogenase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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-1SP / (2S)-pentane-1,2-diol


Mass: 104.148 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN FROM THE RHODOBACTER SPAEROIDES STRAIN D DIFFERS FROM THAT OF STRAIN 2. ...THE SEQUENCE OF THE PROTEIN FROM THE RHODOBACTER SPAEROIDES STRAIN D DIFFERS FROM THAT OF STRAIN 2.4.1 IN THE UNIPROT DATA BASE IN FIVE POSITIONS IN THE SEQUENCE: G54A, E53Q, S61A, A79E, G208E.

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 5.5
Details: 100MM MES PH 5.5, 200MM MAGNESIUM CHLORIDE, 12.5%(W/V)MPEG5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: CCD / 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: 1.95→20 Å / Num. obs: 64019 / % possible obs: 98.5 % / Observed criterion σ(I): 1.8 / Redundancy: 8.9 % / Biso Wilson estimate: 23.51 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 15.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS PROT MODEL

Resolution: 1.95→19.86 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.232 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3240 5.1 %RANDOM
Rwork0.187 ---
obs0.189 60703 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2--
2--0.01 Å2-
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 215 495 8096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227755
X-RAY DIFFRACTIONr_bond_other_d0.0020.025042
X-RAY DIFFRACTIONr_angle_refined_deg1.691.97910569
X-RAY DIFFRACTIONr_angle_other_deg1.1993.00312013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14151018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15622.068295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.447151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7921579
X-RAY DIFFRACTIONr_chiral_restr0.1040.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021645
X-RAY DIFFRACTIONr_nbd_refined0.2050.21631
X-RAY DIFFRACTIONr_nbd_other0.210.25531
X-RAY DIFFRACTIONr_nbtor_refined0.170.23716
X-RAY DIFFRACTIONr_nbtor_other0.0920.24081
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.266
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.2151
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7790.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 235 -
Rwork0.268 4154 -
obs--93.78 %

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