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- PDB-1r66: Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from St... -

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Basic information

Entry
Database: PDB / ID: 1r66
TitleCrystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound
ComponentsTDP-glucose-4,6-dehydratase
KeywordsLYASE / Dehydratase / Rossmann Fold / Short-Chain Dehydrogenase/Reductase
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic 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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex ...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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsAllard, S.T.M. / Cleland, W.W. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae
Authors: Allard, S.T.M. / Cleland, W.W. / Holden, H.M.
History
DepositionOct 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 15, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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: TDP-glucose-4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6014
Polymers36,5001
Non-polymers1,1013
Water4,918273
1
A: TDP-glucose-4,6-dehydratase
hetero molecules

A: TDP-glucose-4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2028
Polymers73,0002
Non-polymers2,2026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6650 Å2
ΔGint-61 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.501, 99.799, 42.187
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-902-

CL

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Components

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


Mass: 36499.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: DesIV / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)PLysS / References: UniProt: Q9ZGH3, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 277 K / Method: batch / pH: 6.3
Details: PEG 8000, magnesium acetate tetrahydrate, sodium cacodylate, pH 6.3, Batch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
220 %PEG800011
3200 mMmagnesium acetate tetrahydrate11
4100 mMsodium cacodylate11pH6.5
57 %PEG800012
6100 mMmagnesium acetate tetrahydrate12
7100 mMsodium cacodylate12pH6.3

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 4, 2002 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. all: 57828 / Num. obs: 56518 / % possible obs: 98.6 % / Redundancy: 5.5 % / Rsym value: 0.066 / Net I/σ(I): 26.4
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 5618 / Rsym value: 0.212 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.44 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 5618 / Rmerge(I) obs: 0.212

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXK

1bxk


Resolution: 1.44→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used weighted least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5729 -RANDOM
Rwork0.176 ---
all-57828 --
obs-56518 99 %-
Refinement stepCycle: LAST / Resolution: 1.44→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 70 273 2818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.34
X-RAY DIFFRACTIONt_bond_d0.013
Software
*PLUS
Version: 'V. 5-E' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 52099 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.4
X-RAY DIFFRACTIONt_planar_d0.015

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