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- PDB-1kc3: Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (Rm... -

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Basic information

Entry
Database: PDB / ID: 1kc3
TitleCrystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose
ComponentsdTDP-glucose oxidoreductase
KeywordsOXIDOREDUCTASE / Rossman-fold / sugar-nucleotide-binding domain
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic process / metal ion binding / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate 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
Chem-NDP / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsBlankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H.
Citation
Journal: Structure / Year: 2002
Title: Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
Authors: Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella ...Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella entrica serovar Typhimurim
Authors: Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Messner, P. / Whitfield, C. / Naismith, J.H.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 2000
Title: The rhamnose pathway
Authors: Giraud, M.F. / Naismith, J.H.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _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-glucose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9084
Polymers32,5901
Non-polymers1,3183
Water1,67593
1
A: dTDP-glucose oxidoreductase
hetero molecules

A: dTDP-glucose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8168
Polymers65,1802
Non-polymers2,6366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7110 Å2
ΔGint-40 kcal/mol
Surface area23850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.980, 72.261, 82.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

MG

DetailsThe biological assembly is a dimer generated by the twofold axis along c: -x, -y, z.

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Components

#1: Protein dTDP-glucose oxidoreductase / E.C.1.1.1.133 / dTDP-6-deoxy-L-lyxo-4-hexulose reductase / DTDP-4-DEHYDRORHAMNOSE REDUCTASE / DTDP-4-KETO-L- ...dTDP-6-deoxy-L-lyxo-4-hexulose reductase / DTDP-4-DEHYDRORHAMNOSE REDUCTASE / DTDP-4-KETO-L-RHAMNOSE REDUCTASE / DTDP-6-DEOXY-L-MANNOSE DEHYDROGENASE / DTDP-L-RHAMNOSE SYNTHETASE / rfbA protein / TDP-rhamnose synthetase


Mass: 32589.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: rfbA / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda DE3)pLysS
References: UniProt: P26392, dTDP-4-dehydrorhamnose reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: HEPES, PEG-MME 5000, MgCl2, pH 6.8, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal grow
*PLUS
pH: 7.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122 %(w/v)PEG40001reservoir
20.1 MHEPES1reservoirpH7.1
30.2 M1reservoirMgCl2
44 mMdithiothreitol1reservoir
52.5 mMNADPH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→28.75 Å / Num. all: 7905 / Num. obs: 7905 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 3.8
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 28521 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.377

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→28.87 Å / SU B: 18.382 / SU ML: 0.364 / SU Rfree: 0.449 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.449 / Stereochemistry target values: Engh & Huber
Details: TLS-option with cofactor-binding, substrate-binding domains and waters as three separate TLS-bodies was used throughout
RfactorNum. reflection% reflectionSelection details
Rfree0.28897 413 5 %RANDOM
Rwork0.191 ---
all0.198697 7806 --
obs0.196 7806 98.67 %-
Displacement parametersBiso mean: 39.02 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å20 Å20 Å2
2---5.28 Å20 Å2
3----0.67 Å2
Refine analyzeLuzzati coordinate error free: 0.449 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 84 93 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021
X-RAY DIFFRACTIONr_angle_refined_deg2.2821.987
X-RAY DIFFRACTIONp_mcbond_it0.9381.5
X-RAY DIFFRACTIONp_mcangle_it1.72
X-RAY DIFFRACTIONp_scbond_it2.2663
X-RAY DIFFRACTIONp_scangle_it3.1954.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 30
Rwork0.214 -
obs-581
Refinement
*PLUS
Rfactor all: 0.198697 / Rfactor obs: 0.196 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.28
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.213

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