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

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Basic information

Entry
Database: PDB / ID: 1kep
TitleThe crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose 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 / nucleotide-sugar metabolic process / dTDP-rhamnose biosynthetic process / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic process / nucleotide binding
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'-DIPHOSPHO-BETA-D-XYLOSE / dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesStreptococcus suis (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 16, 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: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 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

Downloads & links

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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)80,6489
Polymers77,9652
Non-polymers2,6847
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-83 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.449, 97.182, 185.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 38982.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: rmlB / Variant: serotype 2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P95780, UniProt: Q8GIP9*PLUS, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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-TDX / THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE


Mass: 534.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 35% PEG 4000, 0.1M Citric acid pH 5.4, 0.3M ammonium sulphate and 3% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.6 mg/mlprotein1drop
22.5 mMdithiothreitol1drop
34 mMNAD+1drop
47 mMdTDP-xylose1drop
535 %(w/v)PEG40001reservoir
60.1 Mcitric acid1reservoirpH5.4
70.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 / Details: morrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→91.3 Å / Num. all: 102080 / Num. obs: 91826 / % possible obs: 97 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.82 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.079 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12822 / Rsym value: 0.291 / % possible all: 85.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 102080 / % possible obs: 97 % / Num. measured all: 340418 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 85.1 % / Num. unique obs: 12822 / Num. measured obs: 30104 / Rmerge(I) obs: 0.291

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1G1A

1g1a


Resolution: 1.8→91.29 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.17238 10151 10 %RANDOM
Rwork0.14525 ---
obs0.14795 91826 96.83 %-
all-102080 --
Displacement parametersBiso mean: 6.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 149 804 6431
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONp_bond_d0.01957950
X-RAY DIFFRACTIONp_angle_d1.77179071.9
X-RAY DIFFRACTIONp_angle_deg1.77179071.9
X-RAY DIFFRACTIONp_mcbond_it0.80234321.5
X-RAY DIFFRACTIONp_mcangle_it1.47255222
X-RAY DIFFRACTIONp_scbond_it2.56523633
X-RAY DIFFRACTIONp_scangle_it4.13223854.5
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.262 591
Rwork0.225 -
obs-5625
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 91.3 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.28
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg22.47
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg0.84
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.225

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