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- PDB-1dli: THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS... -

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Basic information

Entry
Database: PDB / ID: 1dli
TitleTHE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION
ComponentsUDP-GLUCOSE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / TERNARY COMPLEX / CRYSTALLOGRAPHIC DIMER
Function / homology
Function and homology information


UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding
Similarity search - Function
UDP-glucose 6-dehydrogenase, bacterial type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, bacterial type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsCampbell, R.E. / Mosimann, S.C. / van de Rijn, I. / Tanner, M.E. / Strynadka, N.C.J.
CitationJournal: Biochemistry / Year: 2000
Title: The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation.
Authors: Campbell, R.E. / Mosimann, S.C. / van De Rijn, I. / Tanner, M.E. / Strynadka, N.C.
History
DepositionDec 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3019
Polymers45,5371
Non-polymers1,7648
Water5,044280
1
A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules

A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,60318
Polymers91,0742
Non-polymers3,52816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area12280 Å2
ΔGint-148 kcal/mol
Surface area32090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.601, 106.601, 81.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-GLUCOSE DEHYDROGENASE


Mass: 45537.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: PGAC147 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0F4, UDP-glucose 6-dehydrogenase

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O16P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: AMMONIUM SULPHATE, GLYCEROL, TRIS-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: ambient temperature
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6-1.7 Mammonium sulfate1reservoir
26-8 %glycerol1reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 2.31→24.23 Å / Num. all: 20008 / Num. obs: 20008 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.377 / % possible all: 76.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 24.3 Å / % possible obs: 95.1 % / Num. measured all: 119755 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 76.2 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.31→24.23 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2332306.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2026 10.1 %RANDOM
Rwork0.186 ---
all0.186 20008 --
obs0.186 20008 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.51 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.53 Å20 Å20 Å2
2---9.53 Å20 Å2
3---19.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.31→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 111 280 3594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.262.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 234 9.4 %
Rwork0.246 2246 -
obs--70.5 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 24 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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