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- PDB-3fs8: Crystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose... -

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Basic information

Entry
Database: PDB / ID: 3fs8
TitleCrystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose N-acetyl transferase from Thermoanaerobacterium thermosaccharolyticum in complex with Acetyl-CoA
ComponentsQdtC
KeywordsTRANSFERASE / acetyltransferase / natural product / deoxysugar
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
ACETYL COENZYME *A / THYMINE / QdtC
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SIR / Resolution: 1.7 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)63,5046
Polymers61,6322
Non-polymers1,8714
Water8,971498
1
A: QdtC
hetero molecules

A: QdtC
hetero molecules

A: QdtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2569
Polymers92,4483
Non-polymers2,8076
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 area15370 Å2
ΔGint-45 kcal/mol
Surface area26070 Å2
MethodPISA
2
B: QdtC
hetero molecules

B: QdtC
hetero molecules

B: QdtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2569
Polymers92,4483
Non-polymers2,8076
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15470 Å2
ΔGint-43 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.300, 67.300, 112.400
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-277-

HOH

21A-304-

HOH

31A-370-

HOH

41A-372-

HOH

51A-503-

HOH

61B-382-

HOH

71B-383-

HOH

81B-399-

HOH

91B-460-

HOH

101B-535-

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: E2701-71 / Gene: qdtC / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6TFC6
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG 5000, 0.01M acetyl-CoA, 0.01M dTDP, 0.1M HEPES, 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: Jul 28, 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: 1.7→30 Å / Num. all: 59238 / Num. obs: 59238 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.064
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 8384 / Rsym value: 0.305 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
SOLVEphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: SIR / Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5928 -random
Rwork0.174 ---
all0.178 59147 --
obs0.178 59147 93.9 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 120 498 4718

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