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- PDB-3pjg: Crystal structure of UDP-glucose dehydrogenase from Klebsiella pn... -

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Basic information

Entry
Database: PDB / ID: 3pjg
TitleCrystal structure of UDP-glucose dehydrogenase from Klebsiella pneumoniae complexed with product UDP-glucuronic acid
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase
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
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-glucose 6-dehydrogenase / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, Y.-Y. / Ko, T.-P. / Lin, C.-H. / Chen, W.-H. / Wang, A.H.-J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Conformational change upon product binding to Klebsiella pneumoniae UDP-glucose dehydrogenase: a possible inhibition mechanism for the key enzyme in polymyxin resistance.
Authors: Chen, Y.Y. / Ko, T.P. / Lin, C.H. / Chen, W.H. / Wang, A.H.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 1, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7684
Polymers47,3861
Non-polymers1,3823
Water2,846158
1
A: UDP-glucose 6-dehydrogenase
hetero molecules

A: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5358
Polymers94,7712
Non-polymers2,7646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4610 Å2
ΔGint-33 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.403, 133.403, 187.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-1000-

HOH

21A-1001-

HOH

31A-1002-

HOH

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Components

#1: Protein UDP-glucose 6-dehydrogenase /


Mass: 47385.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: NTUH-K2044 / Gene: KP1_3701, ugd / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C4XAX5, UniProt: A0A0J9WZA6*PLUS, UDP-glucose 6-dehydrogenase
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID / Uridine diphosphate glucuronic acid


Mass: 580.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 5.08 Å3/Da / Density % sol: 75.77 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 11
Details: 20mM CAPS buffer (pH 11.0), 6% (w/v) PEG 8000, 16% (w/v) ethyleneglycol, 4mM UDP-glucuronic acid, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2008 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 27680 / Num. obs: 27652 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 35.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 7.8 / Num. unique all: 2708 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PID

3pid


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1286 -RANDOM
Rwork0.1853 ---
all0.1873 26633 --
obs0.1873 25347 96.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 88 158 3322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.05929
X-RAY DIFFRACTIONc_bond_d0.019963
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.0286
RfactorNum. reflection% reflection
Rfree0.2904 119 -
Rwork0.2618 --
obs-2441 90.34 %

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