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- PDB-1kew: The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) fr... -

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Basic information

Entry
Database: PDB / ID: 1kew
TitleThe crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound
ComponentsdTDP-D-glucose 4,6-dehydratase
KeywordsLYASE / Rossmann fold
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / NADH binding / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic process
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THYMIDINE-5'-DIPHOSPHATE / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAllard, S.T.M. / Beis, K. / Giraud, M.-F. / Hegeman, A.D. / Gross, J.W. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Naismith, J.H.
CitationJournal: Structure / Year: 2002
Title: Toward a structural understanding of the dehydratase mechanism.
Authors: Allard, S.T. / Beis, K. / Giraud, M.F. / Hegeman, A.D. / Gross, J.W. / Wilmouth, R.C. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Maskell, D.J. / Naismith, J.H.
History
DepositionNov 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: dTDP-D-glucose 4,6-dehydratase
B: dTDP-D-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9439
Polymers81,5352
Non-polymers2,4087
Water12,629701
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-55 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.897, 169.897, 92.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein dTDP-D-glucose 4,6-dehydratase / E.C.4.2.1.46 / dTDP-glucose 4 / 6-dehydratase / RmlB


Mass: 40767.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Species: Salmonella enterica / Strain: subsp. enterica serovar Typhimurium / Gene: rmlB / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26391, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 701 / 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: 4.74 Å3/Da / Density % sol: 74.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.32
Details: 0.1M MES pH 6.32, 1.5M lithium sulphate, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
22.5 mMdithiothreitol1drop
34 mMNAD+1drop
410 mMdTDP1drop
50.1 MMES1reservoirpH6.3
61.5 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→44.3 Å / Num. obs: 140877 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.935 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.053 / Net I/σ(I): 8.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1 / Num. unique all: 20513 / Rsym value: 0.185 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 549500 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 99.9 % / Num. unique obs: 20513 / Num. measured obs: 76465 / Rmerge(I) obs: 0.185

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G1A

1g1a


Resolution: 1.8→500 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & HUber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 7022 5 %RANDOM
Rwork0.205 ---
all-140928 --
obs-140818 99.9 %-
Displacement parametersBiso mean: 23.5557 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 156 701 6615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.4312
X-RAY DIFFRACTIONc_dihedral_angle_d22.2012
X-RAY DIFFRACTIONc_improper_angle_d0.8862
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.2896 696 -
Rwork0.2463 --
obs-14068 95.03 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 44.3 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2012
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8862

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