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- PDB-1g1a: THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FRO... -

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Basic information

Entry
Database: PDB / ID: 1g1a
TitleTHE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM
ComponentsDTDP-D-GLUCOSE 4,6-DEHYDRATASE
KeywordsLYASE / Rossmann fold / Protein-NAD complex / Short Chain Dehydrogenase
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / NADH binding / 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 / dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsAllard, S.T.M. / Giraud, M.-F. / Whitfield, C. / Graninger, M. / Messner, P. / Naismith, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway.
Authors: Allard, S.T. / Giraud, M.F. / Whitfield, C. / Graninger, M. / Messner, P. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The purifiaction, crystallisation and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar Typhimurium.
Authors: Allard, S.T.M. / Giraud, M.-F. / Whitfield, C. / Messner, P. / Naismith, J.H.
History
DepositionOct 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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
C: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
D: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,58817
Polymers163,0704
Non-polymers3,51813
Water9,224512
1
A: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
B: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3429
Polymers81,5352
Non-polymers1,8077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-95 kcal/mol
Surface area27810 Å2
MethodPISA
2
C: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
D: DTDP-D-GLUCOSE 4,6-DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2468
Polymers81,5352
Non-polymers1,7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-80 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.623, 87.533, 111.304
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological unit is a dimer. The assymmmetric unit contains two dimers.

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Components

#1: Protein
DTDP-D-GLUCOSE 4,6-DEHYDRATASE / E.C.4.2.1.46


Mass: 40767.516 Da / Num. of mol.: 4
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 / Variant: SEROVAR TYPHIMURIUM / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli)
References: UniProt: P26391, UniProt: Q9EU31*PLUS, dTDP-glucose 4,6-dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1M MES, 1.5M lithium Sulfate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
22.5 mMNAD+1drop
34 mMdithiothreitol1drop
40.1 MMES1reservoir
51.5 Mlithium sulphate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSRS PX7.211.488
SYNCHROTRONESRF BM1420.934
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJul 7, 1999
MARRESEARCH2CCDFeb 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
20.9341
ReflectionResolution: 2.47→40.8 Å / Num. all: 74855 / Num. obs: 67669 / % possible obs: 90.4 % / Redundancy: 3 % / Biso Wilson estimate: 44.217 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.358 / Num. unique all: 7903 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 201143
Reflection shell
*PLUS
% possible obs: 72.9 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.47→40.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3391 5 %Random
Rwork0.202 ---
all0.204 74855 --
obs0.204 67669 90.4 %-
Refinement stepCycle: LAST / Resolution: 2.47→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11196 0 221 512 11929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.44
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.43
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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