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- PDB-3phl: The apo-form UDP-glucose 6-dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3phl
TitleThe apo-form UDP-glucose 6-dehydrogenase
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 / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UDP-glucose 6-dehydrogenase / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 4, 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 13, 2019Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose 6-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)47,3861
Polymers47,3861
Non-polymers00
Water8,503472
1
A: UDP-glucose 6-dehydrogenase

A: UDP-glucose 6-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)94,7712
Polymers94,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5080 Å2
ΔGint-40 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.937, 63.727, 78.124
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

21A-1000-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris-HCl buffer (pH 8.0), 0.8M sodium formate, 19-25 % (w/v) PEG 2000 monomethyl ether., VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 22, 2009 / 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: 1.9→30 Å / Num. all: 38066 / Num. obs: 37761 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.5 / Num. unique all: 14460 / % possible all: 99.7

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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: 1DLI

1dli


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1801 -RANDOM
Rwork0.1754 ---
all0.1777 36205 --
obs0.1777 34404 94.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 472 3466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.77783
X-RAY DIFFRACTIONc_bond_d0.020207
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.0627
RfactorNum. reflection% reflection
Rfree0.305 173 -
Rwork0.2423 --
obs-3234 85.72 %

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