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- PDB-3fsb: Crystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose... -

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Basic information

Entry
Database: PDB / ID: 3fsb
TitleCrystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose N-acetyl transferase from Thermoanaerobacterium thermosaccharolyticum in complex with CoA and dTDP-3-amino-quinovose
ComponentsQdtC
KeywordsTRANSFERASE / N-acetyltransferase / deoxysugar / natural product
Function / homology
Function and homology information


Ubiquitin Ligase Nedd4; Chain: W; - #30 / Ubiquitin Ligase Nedd4; Chain: W; / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Other non-globular / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily ...Ubiquitin Ligase Nedd4; Chain: W; - #30 / Ubiquitin Ligase Nedd4; Chain: W; / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Other non-globular / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Special / Mainly Beta
Similarity search - Domain/homology
COENZYME A / Chem-T3Q / QdtC
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and Functional Studies of QdtC: an N-Acetyltransferase Required for the Biosynthesis of dTDP-3-Acetamido-3,6-Dideoxy-alpha-D-Glucose.
Authors: Thoden, J. / Cook, P. / Schaffer, C. / Messner, P. / Holden, H.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QdtC
B: QdtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2626
Polymers61,6322
Non-polymers2,6304
Water4,125229
1
A: QdtC
hetero molecules

A: QdtC
hetero molecules

A: QdtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3939
Polymers92,4483
Non-polymers3,9456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15090 Å2
ΔGint-52 kcal/mol
Surface area25970 Å2
MethodPISA
2
B: QdtC
hetero molecules

B: QdtC
hetero molecules

B: QdtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3939
Polymers92,4483
Non-polymers3,9456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area14930 Å2
ΔGint-46 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.600, 67.600, 112.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21A-289-

HOH

31A-348-

HOH

41A-349-

HOH

51B-340-

HOH

61B-348-

HOH

71B-387-

HOH

81B-391-

HOH

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Components

#1: Protein QdtC


Mass: 30816.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (bacteria)
Strain: E2707-71 / Gene: qdtC / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6TFC6
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-T3Q / [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose


Mass: 547.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG 5000, 0.1M HEPES, 0.01 M Acetyl-CoA, 0.04M dTDP-3-aminoquinovose, 2% ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker AXS Platinum135 / Detector: CCD / Date: Aug 1, 2008 / Details: Montel
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 39913 / Num. obs: 39913 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.084
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4815 / Rsym value: 0.264 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fs8

3fs8


Resolution: 1.95→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3986 -random
Rwork0.183 ---
all0.185 39903 --
obs0.185 39903 95.1 %-
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 166 229 4510

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