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

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Basic information

Entry
Database: PDB / ID: 1dlj
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)47,3319
Polymers45,5211
Non-polymers1,8108
Water7,098394
1
A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules

A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,66318
Polymers91,0422
Non-polymers3,62016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area12490 Å2
ΔGint-148 kcal/mol
Surface area32360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.961, 106.961, 81.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21A-601-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-GLUCOSE DEHYDROGENASE


Mass: 45521.059 Da / Num. of mol.: 1 / Mutation: C260S
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, 402 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
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
12-2.1 Mammonium sulfate1reservoir
26-8 %glycerol1reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→27.9 Å / Num. all: 38487 / Num. obs: 38487 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / % possible all: 42.4
Reflection
*PLUS
% possible obs: 87.3 % / Num. measured all: 176474
Reflection shell
*PLUS
% possible obs: 42.4 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementResolution: 1.8→27.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2357379.26 / 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
Rfree0.213 3906 10.1 %RANDOM
Rwork0.179 ---
all0.179 38487 --
obs0.179 38487 86.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.72 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.33 Å20 Å20 Å2
2---6.33 Å20 Å2
3---12.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 114 394 3711
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 406 10.7 %
Rwork0.276 3386 -
obs--52.1 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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