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- PDB-1zem: Crystal Structure of NAD+-Bound Xylitol Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1zem
TitleCrystal Structure of NAD+-Bound Xylitol Dehydrogenase
Componentsxylitol dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / Dinucleotide-binding domain
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Xylitol dehydrogenase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEhrensberger, A.H. / Elling, R.A. / Wilson, D.K.
CitationJournal: Structure / Year: 2006
Title: Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity.
Authors: Ehrensberger, A.H. / Elling, R.A. / Wilson, D.K.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_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: xylitol dehydrogenase
B: xylitol dehydrogenase
C: xylitol dehydrogenase
D: xylitol dehydrogenase
E: xylitol dehydrogenase
F: xylitol dehydrogenase
G: xylitol dehydrogenase
H: xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,27521
Polymers222,8468
Non-polymers5,42913
Water29,6891648
1
A: xylitol dehydrogenase
B: xylitol dehydrogenase
C: xylitol dehydrogenase
D: xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,15011
Polymers111,4234
Non-polymers2,7277
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17130 Å2
ΔGint-113 kcal/mol
Surface area32810 Å2
MethodPISA
2
E: xylitol dehydrogenase
F: xylitol dehydrogenase
G: xylitol dehydrogenase
H: xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,12510
Polymers111,4234
Non-polymers2,7026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17060 Å2
ΔGint-111 kcal/mol
Surface area32870 Å2
MethodPISA
3
A: xylitol dehydrogenase
B: xylitol dehydrogenase
C: xylitol dehydrogenase
D: xylitol dehydrogenase
hetero molecules

E: xylitol dehydrogenase
F: xylitol dehydrogenase
G: xylitol dehydrogenase
H: xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,27521
Polymers222,8468
Non-polymers5,42913
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area35020 Å2
ΔGint-224 kcal/mol
Surface area64850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.959, 64.717, 168.239
Angle α, β, γ (deg.)90.00, 93.06, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a tetramer. Each asymmetric unit contains two tetramers.

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Components

#1: Protein
xylitol dehydrogenase


Mass: 27855.748 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: AB091690 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q8GR61, D-xylulose reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1648 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, MgCl2, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.953695 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2004
Details: Flat mirror (vertical focusing) Single crystal bent monochromator (horizontal focusing)
RadiationMonochromator: Si 311 Bent Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 149237 / Num. obs: 137448 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.16 / Num. unique all: 12419 / % possible all: 84

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1IY8 (Levodione Reductase)

1iy8


Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6553 -Random
Rwork0.167 ---
all0.17 149161 --
obs0.17 129843 87 %-
Displacement parametersBiso mean: 17.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15512 0 357 1648 17517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.93437
X-RAY DIFFRACTIONc_bond_d0.01945

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