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- PDB-1r6d: Crystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydr... -

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Basic information

Entry
Database: PDB / ID: 1r6d
TitleCrystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and DAU 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
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 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: Version format compliance
Revision 1.3May 23, 2012Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7263
Polymers36,4981
Non-polymers1,2282
Water6,684371
1
A: TDP-glucose-4,6-dehydratase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)75,4516
Polymers72,9962
Non-polymers2,4564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)71.700, 99.400, 42.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsThe biological assembly is a dimer, contructed from chain A (a symmetry partner generated by the two-fold).

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Components

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


Mass: 36497.918 Da / Num. of mol.: 1 / Mutation: D128N/E129Q
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-DAU / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.6 %
Crystal growTemperature: 277 K / Method: batch macro-seeding / pH: 6.5
Details: Peg 8000, magnesium chloride, cacodylate, pH 6.5, Batch macro-seeding, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMdTDP-glucose1drop
320 %PEG80001reservoir
4200 mMmagnesium acetate tetrahydrate1reservoir
5100 mMsodium cacodylate1reservoirpH6.5
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Aug 13, 2003 / Details: Gobel focusing optics
RadiationMonochromator: GOEBEL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 61664 / Num. obs: 61664 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Rsym value: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.35→1.41 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 6573 / Rsym value: 0.223 / % possible all: 81
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 81 % / Num. unique obs: 6573 / Rmerge(I) obs: 0.223

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Processing

Software
NameClassification
FRAMBOdata collection
XSCALIBREdata reduction
AMoREphasing
TNTrefinement
XSCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R66

1r66


Resolution: 1.35→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6187 -RANDOM
Rwork0.174 ---
all0.176 61664 --
obs0.176 61664 91.9 %-
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 80 371 2926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.35
X-RAY DIFFRACTIONt_bond_d0.014
Refinement
*PLUS
Num. reflection obs: 55477
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.3
X-RAY DIFFRACTIONt_planar_d0.013

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